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Gambino S, Quaglia FM, Galasso M, Cavallini C, Chignola R, Lovato O, Giacobazzi L, Caligola S, Adamo A, Putta S, Aparo A, Ferrarini I, Ugel S, Giugno R, Donadelli M, Dando I, Krampera M, Visco C, Scupoli MT. B-cell receptor signaling activity identifies patients with mantle cell lymphoma at higher risk of progression. Sci Rep 2024; 14:6595. [PMID: 38503806 PMCID: PMC10951201 DOI: 10.1038/s41598-024-55728-9] [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: 10/31/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024] Open
Abstract
Mantle cell lymphoma (MCL) is an incurable B-cell malignancy characterized by a high clinical variability. Therefore, there is a critical need to define parameters that identify high-risk patients for aggressive disease and therapy resistance. B-cell receptor (BCR) signaling is crucial for MCL initiation and progression and is a target for therapeutic intervention. We interrogated BCR signaling proteins (SYK, LCK, BTK, PLCγ2, p38, AKT, NF-κB p65, and STAT5) in 30 primary MCL samples using phospho-specific flow cytometry. Anti-IgM modulation induced heterogeneous BCR signaling responses among samples allowing the identification of two clusters with differential responses. The cluster with higher response was associated with shorter progression free survival (PFS) and overall survival (OS). Moreover, higher constitutive AKT activity was predictive of inferior response to the Bruton's tyrosine kinase inhibitor (BTKi) ibrutinib. Time-to-event analyses showed that MCL international prognostic index (MIPI) high-risk category and higher STAT5 response were predictors of shorter PFS and OS whilst MIPI high-risk category and high SYK response predicted shorter OS. In conclusion, we identified BCR signaling properties associated with poor clinical outcome and resistance to ibrutinib, thus highlighting the prognostic and predictive significance of BCR activity and advancing our understanding of signaling heterogeneity underlying clinical behavior of MCL.
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Affiliation(s)
- Simona Gambino
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy
| | | | - Marilisa Galasso
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy
| | - Chiara Cavallini
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Roberto Chignola
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Ornella Lovato
- Research Center LURM (Interdepartmental Laboratory of Medical Research), University of Verona, Verona, Italy
| | - Luca Giacobazzi
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | | | - Annalisa Adamo
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | | | - Antonino Aparo
- Research Center LURM (Interdepartmental Laboratory of Medical Research), University of Verona, Verona, Italy
| | - Isacco Ferrarini
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy
- Hematology Unit, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Stefano Ugel
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Ilaria Dando
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Mauro Krampera
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy
- Hematology Unit, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Carlo Visco
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy.
- Hematology Unit, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy.
| | - Maria Teresa Scupoli
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy.
- Research Center LURM (Interdepartmental Laboratory of Medical Research), University of Verona, Verona, Italy.
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2
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Di Camillo B, Giugno R. From translational bioinformatics computational methodologies to personalized medicine. J Biomed Inform 2024; 151:104619. [PMID: 38423265 DOI: 10.1016/j.jbi.2024.104619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024]
Affiliation(s)
- Barbara Di Camillo
- Department of Information Engineering - Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy.
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy.
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3
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Cruciani F, Aparo A, Brusini L, Combi C, Storti SF, Giugno R, Menegaz G, Boscolo Galazzo I. Identifying the joint signature of brain atrophy and gene variant scores in Alzheimer's Disease. J Biomed Inform 2024; 149:104569. [PMID: 38104851 DOI: 10.1016/j.jbi.2023.104569] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023]
Abstract
The joint modeling of genetic data and brain imaging information allows for determining the pathophysiological pathways of neurodegenerative diseases such as Alzheimer's disease (AD). This task has typically been approached using mass-univariate methods that rely on a complete set of Single Nucleotide Polymorphisms (SNPs) to assess their association with selected image-derived phenotypes (IDPs). However, such methods are prone to multiple comparisons bias and, most importantly, fail to account for potential cross-feature interactions, resulting in insufficient detection of significant associations. Ways to overcome these limitations while reducing the number of traits aim at conveying genetic information at the gene level and capturing the integrated genetic effects of a set of genetic variants, rather than looking at each SNP individually. Their associations with brain IDPs are still largely unexplored in the current literature, though they can uncover new potential genetic determinants for brain modulations in the AD continuum. In this work, we explored an explainable multivariate model to analyze the genetic basis of the grey matter modulations, relying on the AD Neuroimaging Initiative (ADNI) phase 3 dataset. Cortical thicknesses and subcortical volumes derived from T1-weighted Magnetic Resonance were considered to describe the imaging phenotypes. At the same time the genetic counterpart was represented by gene variant scores extracted by the Sequence Kernel Association Test (SKAT) filtering model. Moreover, transcriptomic analysis was carried on to assess the expression of the resulting genes in the main brain structures as a form of validation. Results highlighted meaningful genotype-phenotype interactionsas defined by three latent components showing a significant difference in the projection scores between patients and controls. Among the significant associations, the model highlighted EPHX1 and BCAS1 gene variant scores involved in neurodegenerative and myelination processes, hence relevant for AD. In particular, the first was associated with decreased subcortical volumes and the second with decreasedtemporal lobe thickness. Noteworthy, BCAS1 is particularly expressed in the dentate gyrus. Overall, the proposed approach allowed capturing genotype-phenotype interactions in a restricted study cohort that was confirmed by transcriptomic analysis, offering insights into the underlying mechanisms of neurodegeneration in AD in line with previous findings and suggesting new potential disease biomarkers.
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Affiliation(s)
- Federica Cruciani
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy.
| | - Antonino Aparo
- Department of Computer Science, University of Verona, Verona, Italy
| | - Lorenza Brusini
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Carlo Combi
- Department of Computer Science, University of Verona, Verona, Italy
| | - Silvia F Storti
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Gloria Menegaz
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
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4
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Mussalo L, Avesani S, Shahbaz MA, Závodná T, Saveleva L, Järvinen A, Lampinen R, Belaya I, Krejčík Z, Ivanova M, Hakkarainen H, Kalapudas J, Penttilä E, Löppönen H, Koivisto AM, Malm T, Topinka J, Giugno R, Aakko-Saksa P, Chew S, Rönkkö T, Jalava P, Kanninen KM. Emissions from modern engines induce distinct effects in human olfactory mucosa cells, depending on fuel and aftertreatment. Sci Total Environ 2023; 905:167038. [PMID: 37709087 DOI: 10.1016/j.scitotenv.2023.167038] [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: 06/16/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Ultrafine particles (UFP) with a diameter of ≤0.1 μm, are contributors to ambient air pollution and derived mainly from traffic emissions, yet their health effects remain poorly characterized. The olfactory mucosa (OM) is located at the rooftop of the nasal cavity and directly exposed to both the environment and the brain. Mounting evidence suggests that pollutant particles affect the brain through the olfactory tract, however, the exact cellular mechanisms of how the OM responds to air pollutants remain poorly known. Here we show that the responses of primary human OM cells are altered upon exposure to UFPs and that different fuels and engines elicit different adverse effects. We used UFPs collected from exhausts of a heavy-duty-engine run with renewable diesel (A0) and fossil diesel (A20), and from a modern diesel vehicle run with renewable diesel (Euro6) and compared their health effects on the OM cells by assessing cellular processes on the functional and transcriptomic levels. Quantification revealed all samples as UFPs with the majority of particles being ≤0.1 μm by an aerodynamic diameter. Exposure to A0 and A20 induced substantial alterations in processes associated with inflammatory response, xenobiotic metabolism, olfactory signaling, and epithelial integrity. Euro6 caused only negligible changes, demonstrating the efficacy of aftertreatment devices. Furthermore, when compared to A20, A0 elicited less pronounced effects on OM cells, suggesting renewable diesel induces less adverse effects in OM cells. Prior studies and these results suggest that PAHs may disturb the inflammatory process and xenobiotic metabolism in the OM and that UFPs might mediate harmful effects on the brain through the olfactory route. This study provides important information on the adverse effects of UFPs in a human-based in vitro model, therefore providing new insight to form the basis for mitigation and preventive actions against the possible toxicological impairments caused by UFP exposure.
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Affiliation(s)
- Laura Mussalo
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Simone Avesani
- Department of Computer Science, University of Verona, 37134 Verona, Italy
| | - Muhammad Ali Shahbaz
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Táňa Závodná
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Liudmila Saveleva
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Anssi Järvinen
- VTT Technical Research Centre of Finland, VTT, 02044 Espoo, Finland
| | - Riikka Lampinen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Irina Belaya
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Zdeněk Krejčík
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Mariia Ivanova
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Henri Hakkarainen
- Inhalation Toxicology Laboratory, Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Juho Kalapudas
- Department of Neurology, Neuro Centre, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Elina Penttilä
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Heikki Löppönen
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Anne M Koivisto
- Department of Neurology, Neuro Centre, Kuopio University Hospital, 70210 Kuopio, Finland; Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; Department of Neurology and Geriatrics, Helsinki University Hospital and Neurosciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Tarja Malm
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, 37134 Verona, Italy
| | | | - Sweelin Chew
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Topi Rönkkö
- Aerosol Physics Laboratory, Physics Unit, Tampere University, 33014 Tampere, Finland
| | - Pasi Jalava
- Inhalation Toxicology Laboratory, Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Katja M Kanninen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland.
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5
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Bonnici V, Mengoni C, Mangoni M, Franco G, Giugno R. PanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies. J Biomed Inform 2023; 148:104552. [PMID: 37995844 DOI: 10.1016/j.jbi.2023.104552] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/06/2023] [Accepted: 11/19/2023] [Indexed: 11/25/2023]
Abstract
Pangenomics was originally defined as the problem of comparing the composition of genes into gene families within a set of bacterial isolates belonging to the same species. The problem requires the calculation of sequence homology among such genes. When combined with metagenomics, namely for human microbiome composition analysis, gene-oriented pangenome detection becomes a promising method to decipher ecosystem functions and population-level evolution. Established computational tools are able to investigate the genetic content of isolates for which a complete genomic sequence is available. However, there is a plethora of incomplete genomes that are available on public resources, which only a few tools may analyze. Incomplete means that the process for reconstructing their genomic sequence is not complete, and only fragments of their sequence are currently available. However, the information contained in these fragments may play an essential role in the analyses. Here, we present PanDelos-frags, a computational tool which exploits and extends previous results in analyzing complete genomes. It provides a new methodology for inferring missing genetic information and thus for managing incomplete genomes. PanDelos-frags outperforms state-of-the-art approaches in reconstructing gene families in synthetic benchmarks and in a real use case of metagenomics. PanDelos-frags is publicly available at https://github.com/InfOmics/PanDelos-frags.
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Affiliation(s)
- Vincenzo Bonnici
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 53/a (Campus), Parma, 43124, PR, Italy.
| | - Claudia Mengoni
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, 37134, VR, Italy
| | - Manuel Mangoni
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy; Department of Experimental Medicine, Sapienza University of Rome, Rome (RM), Italy
| | - Giuditta Franco
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, 37134, VR, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, 37134, VR, Italy
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6
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Viesi E, Sardina DS, Perricone U, Giugno R. APDB: a database on air pollutant characterization and similarity prediction. Database (Oxford) 2023; 2023:baad046. [PMID: 37450416 PMCID: PMC10348400 DOI: 10.1093/database/baad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/12/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
The World Health Organization estimates that 9 out of 10 people worldwide breathe air containing high levels of pollutants. Long-term and chronic exposure to high concentrations of air pollutants is associated with deleterious effects on vital organs, including increased inflammation in the lungs, oxidative stress in the heart and disruption of the blood-brain barrier. For this reason, in an effort to find an association between exposure to pollutants and the toxicological effects observable on human health, an online resource collecting and characterizing in detail pollutant molecules could be helpful to investigate their properties and mechanisms of action. We developed a database, APDB, collecting air-pollutant-related data from different online resources, in particular, molecules from the US Environmental Protection Agency, their associated targets and bioassays found in the PubChem chemical repository and their computed molecular descriptors and quantum mechanics properties. A web interface allows (i) to browse data by category, (ii) to navigate the database by querying molecules and targets and (iii) to visualize and download molecule and target structures as well as computed descriptors and similarities. The desired data can be freely exported in textual/tabular format and the whole database in SQL format. Database URL http://apdb.di.univr.it.
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Affiliation(s)
- Eva Viesi
- Department of Computer Science, University of Verona, Strada le Grazie 15, Verona 37134, Italy
| | - Davide Stefano Sardina
- Molecular Informatics Unit, Ri.MED Foundation, Via Filippo Marini 14, Palermo 90128, Italy
| | - Ugo Perricone
- Molecular Informatics Unit, Ri.MED Foundation, Via Filippo Marini 14, Palermo 90128, Italy
- National Biodiversity Future Center (NBFC), Piazza Marina 61, Palermo 90133, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie 15, Verona 37134, Italy
- National Biodiversity Future Center (NBFC), Piazza Marina 61, Palermo 90133, Italy
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7
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Heer M, Giudice L, Mengoni C, Giugno R, Rico D. Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers. Nucleic Acids Res 2023; 51:e55. [PMID: 37021559 PMCID: PMC10250221 DOI: 10.1093/nar/gkad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 03/06/2023] [Accepted: 04/03/2023] [Indexed: 04/07/2023] Open
Abstract
Most cell type-specific genes are regulated by the interaction of enhancers with their promoters. The identification of enhancers is not trivial as enhancers are diverse in their characteristics and dynamic in their interaction partners. We present Esearch3D, a new method that exploits network theory approaches to identify active enhancers. Our work is based on the fact that enhancers act as a source of regulatory information to increase the rate of transcription of their target genes and that the flow of this information is mediated by the folding of chromatin in the three-dimensional (3D) nuclear space between the enhancer and the target gene promoter. Esearch3D reverse engineers this flow of information to calculate the likelihood of enhancer activity in intergenic regions by propagating the transcription levels of genes across 3D genome networks. Regions predicted to have high enhancer activity are shown to be enriched in annotations indicative of enhancer activity. These include: enhancer-associated histone marks, bidirectional CAGE-seq, STARR-seq, P300, RNA polymerase II and expression quantitative trait loci (eQTLs). Esearch3D leverages the relationship between chromatin architecture and transcription, allowing the prediction of active enhancers and an understanding of the complex underpinnings of regulatory networks. The method is available at: https://github.com/InfOmics/Esearch3D and https://doi.org/10.5281/zenodo.7737123.
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Affiliation(s)
- Maninder Heer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Luca Giudice
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Claudia Mengoni
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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8
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Tognon M, Giugno R, Pinello L. A survey on algorithms to characterize transcription factor binding sites. Brief Bioinform 2023; 24:bbad156. [PMID: 37099664 PMCID: PMC10422928 DOI: 10.1093/bib/bbad156] [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: 01/13/2023] [Revised: 03/27/2023] [Accepted: 04/01/2023] [Indexed: 04/28/2023] Open
Abstract
Transcription factors (TFs) are key regulatory proteins that control the transcriptional rate of cells by binding short DNA sequences called transcription factor binding sites (TFBS) or motifs. Identifying and characterizing TFBS is fundamental to understanding the regulatory mechanisms governing the transcriptional state of cells. During the last decades, several experimental methods have been developed to recover DNA sequences containing TFBS. In parallel, computational methods have been proposed to discover and identify TFBS motifs based on these DNA sequences. This is one of the most widely investigated problems in bioinformatics and is referred to as the motif discovery problem. In this manuscript, we review classical and novel experimental and computational methods developed to discover and characterize TFBS motifs in DNA sequences, highlighting their advantages and drawbacks. We also discuss open challenges and future perspectives that could fill the remaining gaps in the field.
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Affiliation(s)
- Manuel Tognon
- Computer Science Department, University of Verona, Verona, Italy
- Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Rosalba Giugno
- Computer Science Department, University of Verona, Verona, Italy
| | - Luca Pinello
- Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
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Cho WC, Pérez-Tur J, Giugno R, Pirooznia M, Boris-Lawrie K, Greenbaum D, Rastegar M, Henrique R, Xu P, da Rocha JBT, Rogina B. Editorial: 10 years of Frontiers in genetics: past discoveries, current challenges and future perspectives. Front Genet 2023; 14:1192071. [PMID: 37214417 PMCID: PMC10196458 DOI: 10.3389/fgene.2023.1192071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Affiliation(s)
| | - Jordi Pérez-Tur
- Institut de Biomedicina de València-CSIC, CIBER-CIBERNED, ISCIII, Valencia, Spain
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | | | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
| | - Dov Greenbaum
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Zvi Meitar Institute for Legal Implications of Emerging Technologies, Reichman University, Herzliya, Israel
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Rui Henrique
- Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Por-to.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto (ICBAS-UP), Porto, Portugal
| | - Peng Xu
- Xiamen University, Xiamen, China
| | | | - Blanka Rogina
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
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Korvenlaita N, Gómez‐Budia M, Scoyni F, Pistono C, Giudice L, Eamen S, Loppi S, de Sande AH, Huremagic B, Bouvy‐Liivrand M, Heinäniemi M, Kaikkonen MU, Cheng L, Hill AF, Kanninen KM, Jenster GW, van Royen ME, Ramiro L, Montaner J, Batkova T, Mikulik R, Giugno R, Jolkkonen J, Korhonen P, Malm T. Dynamic release of neuronal extracellular vesicles containing miR-21a-5p is induced by hypoxia. J Extracell Vesicles 2023; 12:e12297. [PMID: 36594832 PMCID: PMC9809533 DOI: 10.1002/jev2.12297] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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] [Indexed: 01/04/2023] Open
Abstract
Hypoxia induces changes in the secretion of extracellular vesicles (EVs) in several non-neuronal cells and pathological conditions. EVs are packed with biomolecules, such as microRNA(miR)-21-5p, which respond to hypoxia. However, the true EV association of miR-21-5p, and its functional or biomarker relevance, are inadequately characterised. Neurons are extremely sensitive cells, and it is not known whether the secretion of neuronal EVs and miR-21-5p are altered upon hypoxia. Here, we characterised the temporal EV secretion profile and cell viability of neurons under hypoxia. Hypoxia induced a rapid increase of miR-21a-5p secretion in the EVs, which preceded the elevation of hypoxia-induced tissue or cellular miR-21a-5p. Prolonged hypoxia induced cell death and the release of morphologically distinct EVs. The EVs protected miR-21a-5p from enzymatic degradation but a remarkable fraction of miR-21a-5p remained fragile and non-EV associated. The increase in miR-21a-5p secretion may have biomarker potential, as high blood levels of miR-21-5p in stroke patients were associated with significant disability at hospital discharge. Our data provides an understanding of the dynamic regulation of EV secretion from neurons under hypoxia and provides a candidate for the prediction of recovery from ischemic stroke.
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Affiliation(s)
- Nea Korvenlaita
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Mireia Gómez‐Budia
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Flavia Scoyni
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Cristiana Pistono
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Luca Giudice
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland,Department of Computer ScienceUniversity of VeronaVeronaVenetoItaly
| | - Shaila Eamen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Sanna Loppi
- Department of ImmunologyUniversity of ArizonaTucsonArizonaUSA
| | - Ana Hernández de Sande
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Benjamin Huremagic
- Department of Computer ScienceUniversity of VeronaVeronaVenetoItaly,Department of Human GeneticsKU LeuvenLeuvenFlandersBelgium
| | | | | | - Minna U. Kaikkonen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Lesley Cheng
- Department of Biochemistry and ChemistrySchool of Agriculture Biomedicine & EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Andrew F. Hill
- Department of Biochemistry and ChemistrySchool of Agriculture Biomedicine & EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia,La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia,Institute for Health and SportVictoria UniversityMelbourneVictoriaAustralia
| | - Katja M. Kanninen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Guido W. Jenster
- Department of UrologyErasmus University Medical CenterRotterdamThe Netherlands
| | - Martin E. van Royen
- Department of PathologyErasmus University Medical CenterRotterdamThe Netherlands
| | - Laura Ramiro
- Neurovascular Research LaboratoryVall d'Hebron Institute of Research (VHIR)Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Joan Montaner
- Neurovascular Research LaboratoryVall d'Hebron Institute of Research (VHIR)Universitat Autònoma de BarcelonaBarcelonaSpain,Institute de Biomedicine of SevilleIBiS/Hospital Universitario Virgen del Rocío/CSIC/University of Seville & Department of NeurologyHospital Universitario Virgen MacarenaSevilleAndalucíaSpain
| | - Tereza Batkova
- BioVendor‐laboratorni medicina a.s.BrnoCzech Republic,International Clinical Research CenterNeurological DepartmentSt. Anne's University Hospital and Masaryk UniversityBrnoCzech Republic
| | - Robert Mikulik
- International Clinical Research CenterNeurological DepartmentSt. Anne's University Hospital and Masaryk UniversityBrnoCzech Republic
| | - Rosalba Giugno
- Department of Computer ScienceUniversity of VeronaVeronaVenetoItaly
| | - Jukka Jolkkonen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Paula Korhonen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Tarja Malm
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
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11
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Cancellieri S, Zeng J, Lin LY, Tognon M, Nguyen MA, Lin J, Bombieri N, Maitland SA, Ciuculescu MF, Katta V, Tsai SQ, Armant M, Wolfe SA, Giugno R, Bauer DE, Pinello L. Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nat Genet 2023; 55:34-43. [PMID: 36522432 PMCID: PMC10272994 DOI: 10.1038/s41588-022-01257-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022]
Abstract
CRISPR gene editing holds great promise to modify DNA sequences in somatic cells to treat disease. However, standard computational and biochemical methods to predict off-target potential focus on reference genomes. We developed an efficient tool called CRISPRme that considers single-nucleotide polymorphism (SNP) and indel genetic variants to nominate and prioritize off-target sites. We tested the software with a BCL11A enhancer targeting guide RNA (gRNA) showing promise in clinical trials for sickle cell disease and β-thalassemia and found that the top candidate off-target is produced by an allele common in African-ancestry populations (MAF 4.5%) that introduces a protospacer adjacent motif (PAM) sequence. We validated that SpCas9 generates strictly allele-specific indels and pericentric inversions in CD34+ hematopoietic stem and progenitor cells (HSPCs), although high-fidelity Cas9 mitigates this off-target. This report illustrates how genetic variants should be considered as modifiers of gene editing outcomes. We expect that variant-aware off-target assessment will become integral to therapeutic genome editing evaluation and provide a powerful approach for comprehensive off-target nomination.
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Affiliation(s)
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Linda Yingqi Lin
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Manuel Tognon
- Department of Computer Science, University of Verona, Verona, Italy
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - My Anh Nguyen
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jiecong Lin
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Nicola Bombieri
- Department of Computer Science, University of Verona, Verona, Italy
| | - Stacy A Maitland
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Varun Katta
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Myriam Armant
- TransLab, Boston Children's Hospital, Boston, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy.
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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12
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Di Camillo B, Giugno R. From translational bioinformatics computational methodologies to personalized medicine. J Biomed Inform 2022; 133:104170. [PMID: 35998813 DOI: 10.1016/j.jbi.2022.104170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Barbara Di Camillo
- Department of Information Engineering, Department of Comparative Biomedicine and Food Science, University of Padova, 35131 Padova, Italy.
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, 37134 Verona, Italy.
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13
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Diaz-Uriarte R, Gómez de Lope E, Giugno R, Fröhlich H, Nazarov PV, Nepomuceno-Chamorro IA, Rauschenberger A, Glaab E. Ten quick tips for biomarker discovery and validation analyses using machine learning. PLoS Comput Biol 2022; 18:e1010357. [PMID: 35951526 PMCID: PMC9371329 DOI: 10.1371/journal.pcbi.1010357] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Ramon Diaz-Uriarte
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid, Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (UAM-CSIC), Madrid, Spain
| | - Elisa Gómez de Lope
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Holger Fröhlich
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
- Bonn-Aachen International Centre for IT (b-it), Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Petr V. Nazarov
- Department of Cancer Research, Luxembourg Institute of Health, Strassen, Luxembourg
| | | | - Armin Rauschenberger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg
- * E-mail:
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14
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Avesani S, Viesi E, Alessandrì L, Motterle G, Bonnici V, Beccuti M, Calogero R, Giugno R. Stardust: improving spatial transcriptomics data analysis through space-aware modularity optimization-based clustering. Gigascience 2022; 11:6659721. [PMID: 35946989 PMCID: PMC9364686 DOI: 10.1093/gigascience/giac075] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/27/2022] [Accepted: 06/30/2022] [Indexed: 01/24/2023] Open
Abstract
Background Spatial transcriptomics (ST) combines stained tissue images with spatially resolved high-throughput RNA sequencing. The spatial transcriptomic analysis includes challenging tasks like clustering, where a partition among data points (spots) is defined by means of a similarity measure. Improving clustering results is a key factor as clustering affects subsequent downstream analysis. State-of-the-art approaches group data by taking into account transcriptional similarity and some by exploiting spatial information as well. However, it is not yet clear how much the spatial information combined with transcriptomics improves the clustering result. Results We propose a new clustering method, Stardust, that easily exploits the combination of space and transcriptomic information in the clustering procedure through a manual or fully automatic tuning of algorithm parameters. Moreover, a parameter-free version of the method is also provided where the spatial contribution depends dynamically on the expression distances distribution in the space. We evaluated the proposed methods results by analyzing ST data sets available on the 10x Genomics website and comparing clustering performances with state-of-the-art approaches by measuring the spots' stability in the clusters and their biological coherence. Stability is defined by the tendency of each point to remain clustered with the same neighbors when perturbations are applied. Conclusions Stardust is an easy-to-use methodology allowing to define how much spatial information should influence clustering on different tissues and achieving more stable results than state-of-the-art approaches.
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Affiliation(s)
- Simone Avesani
- Department of Computer Science, University of Verona, Verona 37134, Italy
| | - Eva Viesi
- Department of Computer Science, University of Verona, Verona 37134, Italy
| | - Luca Alessandrì
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
| | - Giovanni Motterle
- Department of Computer Science, University of Verona, Verona 37134, Italy
| | - Vincenzo Bonnici
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma 43121, Italy
| | - Marco Beccuti
- Department of Computer Science, University of Turin, Turin 10149, Italy
| | - Raffaele Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona 37134, Italy
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15
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Jäntti H, Sitnikova V, Ishchenko Y, Shakirzyanova A, Giudice L, Ugidos IF, Gómez-Budia M, Korvenlaita N, Ohtonen S, Belaya I, Fazaludeen F, Mikhailov N, Gotkiewicz M, Ketola K, Lehtonen Š, Koistinaho J, Kanninen KM, Hernández D, Pébay A, Giugno R, Korhonen P, Giniatullin R, Malm T. Microglial amyloid beta clearance is driven by PIEZO1 channels. J Neuroinflammation 2022; 19:147. [PMID: 35706029 PMCID: PMC9199162 DOI: 10.1186/s12974-022-02486-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [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: 01/18/2022] [Accepted: 05/15/2022] [Indexed: 02/06/2023] Open
Abstract
Background Microglia are the endogenous immune cells of the brain and act as sensors of pathology to maintain brain homeostasis and eliminate potential threats. In Alzheimer's disease (AD), toxic amyloid beta (Aβ) accumulates in the brain and forms stiff plaques. In late-onset AD accounting for 95% of all cases, this is thought to be due to reduced clearance of Aβ. Human genome-wide association studies and animal models suggest that reduced clearance results from aberrant function of microglia. While the impact of neurochemical pathways on microglia had been broadly studied, mechanical receptors regulating microglial functions remain largely unexplored. Methods Here we showed that a mechanotransduction ion channel, PIEZO1, is expressed and functional in human and mouse microglia. We used a small molecule agonist, Yoda1, to study how activation of PIEZO1 affects AD-related functions in human induced pluripotent stem cell (iPSC)-derived microglia-like cells (iMGL) under controlled laboratory experiments. Cell survival, metabolism, phagocytosis and lysosomal activity were assessed using real-time functional assays. To evaluate the effect of activation of PIEZO1 in vivo, 5-month-old 5xFAD male mice were infused daily with Yoda1 for two weeks through intracranial cannulas. Microglial Iba1 expression and Aβ pathology were quantified with immunohistochemistry and confocal microscopy. Published human and mouse AD datasets were used for in-depth analysis of PIEZO1 gene expression and related pathways in microglial subpopulations. Results We show that PIEZO1 orchestrates Aβ clearance by enhancing microglial survival, phagocytosis, and lysosomal activity. Aβ inhibited PIEZO1-mediated calcium transients, whereas activation of PIEZO1 with a selective agonist, Yoda1, improved microglial phagocytosis resulting in Aβ clearance both in human and mouse models of AD. Moreover, PIEZO1 expression was associated with a unique microglial transcriptional phenotype in AD as indicated by assessment of cellular metabolism, and human and mouse single-cell datasets. Conclusion These results indicate that the compromised function of microglia in AD could be improved by controlled activation of PIEZO1 channels resulting in alleviated Aβ burden. Pharmacological regulation of these mechanoreceptors in microglia could represent a novel therapeutic paradigm for AD. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-022-02486-y.
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Affiliation(s)
- Henna Jäntti
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Valeriia Sitnikova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Yevheniia Ishchenko
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland.,Departments of Molecular Biophysics and Biochemistry and Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Anastasia Shakirzyanova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Luca Giudice
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland.,Department of Computer Science, University of Verona, 37134, Verona, Italy
| | - Irene F Ugidos
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Mireia Gómez-Budia
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Nea Korvenlaita
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Sohvi Ohtonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Irina Belaya
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Feroze Fazaludeen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Nikita Mikhailov
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Maria Gotkiewicz
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Kirsi Ketola
- Institute of Biomedicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Šárka Lehtonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland.,Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Jari Koistinaho
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland.,Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Damian Hernández
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia.,Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, 37134, Verona, Italy
| | - Paula Korhonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Rashid Giniatullin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland.
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16
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Lampinen R, Górová V, Avesani S, Liddell JR, Penttilä E, Závodná T, Krejčík Z, Lehtola JM, Saari T, Kalapudas J, Hannonen S, Löppönen H, Topinka J, Koivisto AM, White AR, Giugno R, Kanninen KM. Biometal Dyshomeostasis in Olfactory Mucosa of Alzheimer's Disease Patients. Int J Mol Sci 2022; 23:ijms23084123. [PMID: 35456941 PMCID: PMC9032618 DOI: 10.3390/ijms23084123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 02/28/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/12/2022] Open
Abstract
Olfactory function, orchestrated by the cells of the olfactory mucosa at the rooftop of the nasal cavity, is disturbed early in the pathogenesis of Alzheimer's disease (AD). Biometals including zinc and calcium are known to be important for sense of smell and to be altered in the brains of AD patients. Little is known about elemental homeostasis in the AD patient olfactory mucosa. Here we aimed to assess whether the disease-related alterations to biometal homeostasis observed in the brain are also reflected in the olfactory mucosa. We applied RNA sequencing to discover gene expression changes related to metals in olfactory mucosal cells of cognitively healthy controls, individuals with mild cognitive impairment and AD patients, and performed analysis of the elemental content to determine metal levels. Results demonstrate that the levels of zinc, calcium and sodium are increased in the AD olfactory mucosa concomitantly with alterations to 17 genes related to metal-ion binding or metal-related function of the protein product. A significant elevation in alpha-2-macroglobulin, a known metal-binding biomarker correlated with brain disease burden, was observed on the gene and protein levels in the olfactory mucosa cells of AD patients. These data demonstrate that the olfactory mucosa cells derived from AD patients recapitulate certain impairments of biometal homeostasis observed in the brains of patients.
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Affiliation(s)
- Riikka Lampinen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland; (R.L.); (V.G.)
| | - Veronika Górová
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland; (R.L.); (V.G.)
| | - Simone Avesani
- Department of Computer Science, University of Verona, 37134 Verona, Italy; (S.A.); (R.G.)
| | - Jeffrey R. Liddell
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia;
| | - Elina Penttilä
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland; (E.P.); (H.L.)
| | - Táňa Závodná
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.Z.); (Z.K.); (J.T.)
| | - Zdeněk Krejčík
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.Z.); (Z.K.); (J.T.)
| | - Juha-Matti Lehtola
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; (J.-M.L.); (T.S.); (J.K.); (S.H.); (A.M.K.)
- Department of Neurology, NeuroCentre, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Toni Saari
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; (J.-M.L.); (T.S.); (J.K.); (S.H.); (A.M.K.)
| | - Juho Kalapudas
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; (J.-M.L.); (T.S.); (J.K.); (S.H.); (A.M.K.)
| | - Sanna Hannonen
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; (J.-M.L.); (T.S.); (J.K.); (S.H.); (A.M.K.)
- Department of Neurology, NeuroCentre, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Heikki Löppönen
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland; (E.P.); (H.L.)
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.Z.); (Z.K.); (J.T.)
| | - Anne M. Koivisto
- Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; (J.-M.L.); (T.S.); (J.K.); (S.H.); (A.M.K.)
- Department of Neurology, NeuroCentre, Kuopio University Hospital, 70210 Kuopio, Finland
- Department of Neurology and Geriatrics, Helsinki University Hospital and Neurosciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Anthony R. White
- Department of Cell and Molecular Biology, Mental Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia;
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, 37134 Verona, Italy; (S.A.); (R.G.)
| | - Katja M. Kanninen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland; (R.L.); (V.G.)
- Correspondence:
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17
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Bonnici V, Giugno R. PANPROVA: PANgenomic PROkaryotic eVolution of full Assemblies. Bioinformatics 2022; 38:2631-2632. [PMID: 35289871 DOI: 10.1093/bioinformatics/btac158] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 03/05/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Computational tools for pangenonic analysis have gained increasing interest over the past two decades in various applications such as evolutionary studies and vaccine development. Synthetic benchmarks are essential for the systematic evaluation of their performance. Currently, benchmarking tools represent a genome as a set of genetic sequences and fail to simulate the complete information of the genomes, which is essential for evaluating pangenomic detection between fragmented genomes. RESULTS We present PANPROVA, a benchmark tool to simulate prokaryotic pangenomic evolution by evolving the complete genomic sequence of an ancestral isolate. In this way the possibility of operating in the pre-assembly phase is enabled. Gene set variations, sequence variation and horizontal acquisition from a pool of external genomes are the evolutionary features of the tool. AVAILABILITY AND IMPLEMENTATION PANPROVA is publicly available at https://github.com/InfOmics/PANPROVA.
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Affiliation(s)
- Vincenzo Bonnici
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, 43124, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, 37134, Italy
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18
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De Sanctis F, Lamolinara A, Boschi F, Musiu C, Caligola S, Trovato R, Fiore A, Frusteri C, Anselmi C, Poffe O, Cestari T, Canè S, Sartoris S, Giugno R, Del Rosario G, Zappacosta B, Del Pizzo F, Fassan M, Dugnani E, Piemonti L, Bottani E, Decimo I, Paiella S, Salvia R, Lawlor RT, Corbo V, Park Y, Tuveson DA, Bassi C, Scarpa A, Iezzi M, Ugel S, Bronte V. Interrupting the nitrosative stress fuels tumor-specific cytotoxic T lymphocytes in pancreatic cancer. J Immunother Cancer 2022; 10:jitc-2021-003549. [PMID: 35022194 PMCID: PMC8756272 DOI: 10.1136/jitc-2021-003549] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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] [Accepted: 12/04/2021] [Indexed: 12/11/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest tumors owing to its robust desmoplasia, low immunogenicity, and recruitment of cancer-conditioned, immunoregulatory myeloid cells. These features strongly limit the success of immunotherapy as a single agent, thereby suggesting the need for the development of a multitargeted approach. The goal is to foster T lymphocyte infiltration within the tumor landscape and neutralize cancer-triggered immune suppression, to enhance the therapeutic effectiveness of immune-based treatments, such as anticancer adoptive cell therapy (ACT). Methods We examined the contribution of immunosuppressive myeloid cells expressing arginase 1 and nitric oxide synthase 2 in building up a reactive nitrogen species (RNS)-dependent chemical barrier and shaping the PDAC immune landscape. We examined the impact of pharmacological RNS interference on overcoming the recruitment and immunosuppressive activity of tumor-expanded myeloid cells, which render pancreatic cancers resistant to immunotherapy. Results PDAC progression is marked by a stepwise infiltration of myeloid cells, which enforces a highly immunosuppressive microenvironment through the uncontrolled metabolism of L-arginine by arginase 1 and inducible nitric oxide synthase activity, resulting in the production of large amounts of reactive oxygen and nitrogen species. The extensive accumulation of myeloid suppressing cells and nitrated tyrosines (nitrotyrosine, N-Ty) establishes an RNS-dependent chemical barrier that impairs tumor infiltration by T lymphocytes and restricts the efficacy of adoptive immunotherapy. A pharmacological treatment with AT38 ([3-(aminocarbonyl)furoxan-4-yl]methyl salicylate) reprograms the tumor microenvironment from protumoral to antitumoral, which supports T lymphocyte entrance within the tumor core and aids the efficacy of ACT with telomerase-specific cytotoxic T lymphocytes. Conclusions Tumor microenvironment reprogramming by ablating aberrant RNS production bypasses the current limits of immunotherapy in PDAC by overcoming immune resistance.
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Affiliation(s)
- Francesco De Sanctis
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Alessia Lamolinara
- Department of Neurosciences, Imaging and Clinical Sciences, Center for Advanced Studies and Technnology (CAST), G. d'Annunzio University of Chieti Pescara, Chieti, Italy
| | - Federico Boschi
- Department of Computer Science, University of Verona, Verona, Italy
| | - Chiara Musiu
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Simone Caligola
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Rosalinda Trovato
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Alessandra Fiore
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Cristina Frusteri
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Cristina Anselmi
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Ornella Poffe
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Tiziana Cestari
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Stefania Canè
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Silvia Sartoris
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | | | | | - Francesco Del Pizzo
- Department of Neurosciences, Imaging and Clinical Sciences, Center for Advanced Studies and Technnology (CAST), G. d'Annunzio University of Chieti Pescara, Chieti, Italy
| | - Matteo Fassan
- Department of Medicine, University of Padua, Padova, Italy.,Veneto Institute of Oncology-Institute for Hospitalization and Care Scientific, Padova, Italy
| | - Erica Dugnani
- Diabetes Research Institute, San Raffaele Research Centre, Milano, Italy
| | - Lorenzo Piemonti
- Diabetes Research Institute, San Raffaele Research Centre, Milano, Italy.,School of Medicine and Surgery, Vita-Salute San Raffaele University, Milano, Italy
| | - Emanuela Bottani
- Department of Diagnostic and Public Health, Section of Pharmacology, University of Verona, Verona, Italy
| | - Ilaria Decimo
- Department of Diagnostic and Public Health, Section of Pharmacology, University of Verona, Verona, Italy
| | - Salvatore Paiella
- General and Pancreatic Surgery Unit, University of Verona, Verona, Italy
| | - Roberto Salvia
- General and Pancreatic Surgery Unit, University of Verona, Verona, Italy
| | | | - Vincenzo Corbo
- ARC-NET, University of Verona, Verona, Italy.,Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Youngkyu Park
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Pancreatic Cancer Research Laboratory, Lustgarten Foundation, Cold Spring Harbor, New York, USA
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Pancreatic Cancer Research Laboratory, Lustgarten Foundation, Cold Spring Harbor, New York, USA
| | - Claudio Bassi
- General and Pancreatic Surgery Unit, University of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-NET, University of Verona, Verona, Italy.,Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Manuela Iezzi
- Department of Neurosciences, Imaging and Clinical Sciences, Center for Advanced Studies and Technnology (CAST), G. d'Annunzio University of Chieti Pescara, Chieti, Italy
| | - Stefano Ugel
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Vincenzo Bronte
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
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19
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Martikainen MV, Aakko-Saksa P, van den Broek L, Cassee FR, Carare RO, Chew S, Dinnyes A, Giugno R, Kanninen KM, Malm T, Muala A, Nedergaard M, Oudin A, Oyola P, Pfeiffer TV, Rönkkö T, Saarikoski S, Sandström T, Schins RPF, Topinka J, Yang M, Zeng X, Westerink RHS, Jalava PI. TUBE Project: Transport-Derived Ultrafines and the Brain Effects. Int J Environ Res Public Health 2021; 19:311. [PMID: 35010571 PMCID: PMC8751045 DOI: 10.3390/ijerph19010311] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
The adverse effects of air pollutants on the respiratory and cardiovascular systems are unquestionable. However, in recent years, indications of effects beyond these organ systems have become more evident. Traffic-related air pollution has been linked with neurological diseases, exacerbated cognitive dysfunction, and Alzheimer's disease. However, the exact air pollutant compositions and exposure scenarios leading to these adverse health effects are not known. Although several components of air pollution may be at play, recent experimental studies point to a key role of ultrafine particles (UFPs). While the importance of UFPs has been recognized, almost nothing is known about the smallest fraction of UFPs, and only >23 nm emissions are regulated in the EU. Moreover, the role of the semivolatile fraction of the emissions has been neglected. The Transport-Derived Ultrafines and the Brain Effects (TUBE) project will increase knowledge on harmful ultrafine air pollutants, as well as semivolatile compounds related to adverse health effects. By including all the major current combustion and emission control technologies, the TUBE project aims to provide new information on the adverse health effects of current traffic, as well as information for decision makers to develop more effective emission legislation. Most importantly, the TUBE project will include adverse health effects beyond the respiratory system; TUBE will assess how air pollution affects the brain and how air pollution particles might be removed from the brain. The purpose of this report is to describe the TUBE project, its background, and its goals.
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Affiliation(s)
- Maria-Viola Martikainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70210 Kuopio, Finland; (M.Y.); (P.I.J.)
| | - Päivi Aakko-Saksa
- VTT Technical Research Centre of Finland Ltd., 02044 Espoo, Finland;
| | | | - Flemming R. Cassee
- Centre for Sustainability, Environment and Health, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands;
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, 3508 TD Utrecht, The Netherlands;
| | - Roxana O. Carare
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK;
| | - Sweelin Chew
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland; (S.C.); (K.M.K.); (T.M.)
| | | | - Rosalba Giugno
- Computer Science Department, University of Verona, 37129 Verona, Italy;
| | - Katja M. Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland; (S.C.); (K.M.K.); (T.M.)
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland; (S.C.); (K.M.K.); (T.M.)
| | - Ala Muala
- Department of Public Health and Clinical Medicine, Division of Medicine/Respiratory Medicine, Umeå University, 901 87 Umea, Sweden; (A.M.); (A.O.); (T.S.)
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Anna Oudin
- Department of Public Health and Clinical Medicine, Division of Medicine/Respiratory Medicine, Umeå University, 901 87 Umea, Sweden; (A.M.); (A.O.); (T.S.)
| | - Pedro Oyola
- Centro Mario Molina Chile, Strategic Studies Department, Santiago 602, Chile;
| | | | - Topi Rönkkö
- Aerosol Physics Laboratory, Physics Unit, Faculty of Engineering and Natural Sciences, Tampere University, 33720 Tampere, Finland;
| | - Sanna Saarikoski
- Atmospheric Composition Research, Finnish Meteorological Institute, 00101 Helsinki, Finland;
| | - Thomas Sandström
- Department of Public Health and Clinical Medicine, Division of Medicine/Respiratory Medicine, Umeå University, 901 87 Umea, Sweden; (A.M.); (A.O.); (T.S.)
| | - Roel P. F. Schins
- IUF—Leibniz Research Institute for Environmental Medicine, 40225 Dusseldorf, Germany;
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic;
| | - Mo Yang
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70210 Kuopio, Finland; (M.Y.); (P.I.J.)
| | - Xiaowen Zeng
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China;
| | - Remco H. S. Westerink
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, 3508 TD Utrecht, The Netherlands;
| | - Pasi I. Jalava
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70210 Kuopio, Finland; (M.Y.); (P.I.J.)
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20
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Aparo A, Sala P, Bonnici V, Giugno R. TEDAR: Temporal dynamic signal detection of adverse reactions. Artif Intell Med 2021; 122:102212. [PMID: 34823837 DOI: 10.1016/j.artmed.2021.102212] [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] [Received: 11/27/2020] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 10/19/2022]
Abstract
Computational approaches to detect the signals of adverse drug reactions are powerful tools to monitor the unattended effects that users experience and report, also preventing death and serious injury. They apply statistical indices to affirm the validity of adverse reactions reported by users. The methodologies that scan fixed duration intervals in the lifetime of drugs are among the most used. Here we present a method, called TEDAR, in which ranges of varying length are taken into account. TEDAR has the advantage to detect a greater number of true signals without significantly increasing the number of false positives, which are a major concern for this type of tools. Furthermore, early detection of signals is a key feature of methods to prevent the safety of the population. The results show that TEDAR detects adverse reactions many months earlier than methodologies based on a fixed interval length.
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Affiliation(s)
- Antonino Aparo
- Department of Computer Science, University of Verona, 37134 Strada le Grazie 15, Verona, Italy
| | - Pietro Sala
- Department of Computer Science, University of Verona, 37134 Strada le Grazie 15, Verona, Italy.
| | - Vincenzo Bonnici
- Department of Computer Science, University of Verona, 37134 Strada le Grazie 15, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, 37134 Strada le Grazie 15, Verona, Italy.
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21
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Tognon M, Bonnici V, Garrison E, Giugno R, Pinello L. GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs. PLoS Comput Biol 2021; 17:e1009444. [PMID: 34570769 PMCID: PMC8519448 DOI: 10.1371/journal.pcbi.1009444] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 10/15/2021] [Accepted: 09/10/2021] [Indexed: 11/18/2022] Open
Abstract
Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrences of TFBS in linear DNA sequences or reference genomes, no tool exists to find them in pangenome variation graphs (VGs). VGs are sequence-labelled graphs that can efficiently encode collections of genomes and their variants in a single, compact data structure. Because VGs can losslessly compress large pangenomes, TFBS scanning in VGs can efficiently capture how genomic variation affects the potential binding landscape of TFs in a population of individuals. Here we present GRAFIMO (GRAph-based Finding of Individual Motif Occurrences), a command-line tool for the scanning of known TF DNA motifs represented as Position Weight Matrices (PWMs) in VGs. GRAFIMO extends the standard PWM scanning procedure by considering variations and alternative haplotypes encoded in a VG. Using GRAFIMO on a VG based on individuals from the 1000 Genomes project we recover several potential binding sites that are enhanced, weakened or missed when scanning only the reference genome, and which could constitute individual-specific binding events. GRAFIMO is available as an open-source tool, under the MIT license, at https://github.com/pinellolab/GRAFIMO and https://github.com/InfOmics/GRAFIMO. Transcription factors (TFs) are key regulatory proteins and mutations occurring in their binding sites can alter the normal transcriptional landscape of a cell and lead to disease states. Pangenome variation graphs (VGs) efficiently encode genomes from a population of individuals and their genetic variations. GRAFIMO is an open-source tool that extends the traditional PWM scanning procedure to VGs. By scanning for potential TBFS in VGs, GRAFIMO can simultaneously search thousands of genomes while accounting for SNPs, indels, and structural variants. GRAFIMO reports motif occurrences, their statistical significance, frequency, and location within the reference or alternative haplotypes in a given VG. GRAFIMO makes it possible to study how genetic variation affects the binding landscape of known TFs within a population of individuals.
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Affiliation(s)
- Manuel Tognon
- Computer Science Department, University of Verona, Verona, Italy
| | - Vincenzo Bonnici
- Computer Science Department, University of Verona, Verona, Italy
| | - Erik Garrison
- University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Rosalba Giugno
- Computer Science Department, University of Verona, Verona, Italy
- * E-mail: (RG); (LP)
| | - Luca Pinello
- Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital Charlestown, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (RG); (LP)
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22
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Munz N, Cascione L, Parmigiani L, Tarantelli C, Rinaldi A, Cmiljanovic N, Cmiljanovic V, Giugno R, Bertoni F, Napoli S. Exon-Intron Differential Analysis Reveals the Role of Competing Endogenous RNAs in Post-Transcriptional Regulation of Translation. Noncoding RNA 2021; 7:ncrna7020026. [PMID: 33923420 PMCID: PMC8167571 DOI: 10.3390/ncrna7020026] [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: 01/30/2021] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022] Open
Abstract
Stressful conditions induce the cell to save energy and activate a rescue program modulated by mammalian target of rapamycin (mTOR). Along with transcriptional and translational regulation, the cell relies also on post-transcriptional modulation to quickly adapt the translation of essential proteins. MicroRNAs play an important role in the regulation of protein translation, and their availability is tightly regulated by RNA competing mechanisms often mediated by long noncoding RNAs (lncRNAs). In our paper, we simulated the response to growth adverse condition by bimiralisib, a dual PI3K/mTOR inhibitor, in diffuse large B cell lymphoma cell lines, and we studied post-transcriptional regulation by the differential analysis of exonic and intronic RNA expression. In particular, we observed the upregulation of a lncRNA, lncTNK2-2:1, which correlated with the stabilization of transcripts involved in the regulation of translation and DNA damage after bimiralisib treatment. We identified miR-21-3p as miRNA likely sponged by lncTNK2-2:1, with consequent stabilization of the mRNA of p53, which is a master regulator of cell growth in response to DNA damage.
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Affiliation(s)
- Nicolas Munz
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Luca Parmigiani
- Computer Science Department, University of Verona, 37129 Verona, Italy; (L.P.); (R.G.)
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
| | | | | | - Rosalba Giugno
- Computer Science Department, University of Verona, 37129 Verona, Italy; (L.P.); (R.G.)
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
- Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
- Correspondence:
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23
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Loppi S, Korhonen P, Bouvy‐Liivrand M, Caligola S, Turunen TA, Turunen MP, Hernandez de Sande A, Kołosowska N, Scoyni F, Rosell A, García‐Berrocoso T, Lemarchant S, Dhungana H, Montaner J, Koistinaho J, Kanninen KM, Kaikkonen MU, Giugno R, Heinäniemi M, Malm T. Peripheral inflammation preceeding ischemia impairs neuronal survival through mechanisms involving miR-127 in aged animals. Aging Cell 2021; 20:e13287. [PMID: 33369048 PMCID: PMC7811844 DOI: 10.1111/acel.13287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/22/2019] [Revised: 10/06/2020] [Accepted: 11/27/2020] [Indexed: 01/02/2023] Open
Abstract
Ischemic stroke, the third leading cause of death in the Western world, affects mainly the elderly and is strongly associated with comorbid conditions such as atherosclerosis or diabetes, which are pathologically characterized by increased inflammation and are known to influence the outcome of stroke. Stroke incidence peaks during influenza seasons, and patients suffering from infections such as pneumonia prior to stroke exhibit a worse stroke outcome. Earlier studies have shown that comorbidities aggravate the outcome of stroke, yet the mediators of this phenomenon remain obscure. Here, we show that acute peripheral inflammation aggravates stroke‐induced neuronal damage and motor deficits specifically in aged mice. This is associated with increased levels of plasma proinflammatory cytokines, rather than with an increase of inflammatory mediators in the affected brain parenchyma. Nascent transcriptomics data with mature microRNA sequencing were used to identify the neuron‐specific miRNome, in order to decipher dysregulated miRNAs in the brains of aged animals with stroke and co‐existing inflammation. We pinpoint a previously uninvestigated miRNA in the brain, miR‐127, that is highly neuronal, to be associated with increased cell death in the aged, LPS‐injected ischemic mice. Target prediction tools indicate that miR‐127 interacts with several basally expressed neuronal genes, and of these we verify miR‐127 binding to Psmd3. Finally, we report reduced expression of miR‐127 in human stroke brains. Our results underline the impact of peripheral inflammation on the outcome of stroke in aged subjects and pinpoint molecular targets for restoring endogenous neuronal capacity to combat ischemic stroke.
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Affiliation(s)
- Sanna Loppi
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
- Department of Immunobiology University of Arizona Tucson Arizona USA
| | - Paula Korhonen
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
| | | | - Simone Caligola
- Department of Computer Science University of Verona Verona Italy
| | - Tiia A. Turunen
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
| | - Mikko P. Turunen
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
| | | | - Natalia Kołosowska
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
| | - Flavia Scoyni
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
| | - Anna Rosell
- Neurovascular Research Laboratory Vall d’Hebron Institute of Research (VHIR) Universitat Autònoma de Barcelona Barcelona Spain
| | - Teresa García‐Berrocoso
- Neurovascular Research Laboratory Vall d’Hebron Institute of Research (VHIR) Universitat Autònoma de Barcelona Barcelona Spain
| | - Sighild Lemarchant
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
| | - Hiramani Dhungana
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
- Neuroscience Center University of Helsinki Helsinki Finland
| | - Joan Montaner
- Neurovascular Research Laboratory Vall d’Hebron Institute of Research (VHIR) Universitat Autònoma de Barcelona Barcelona Spain
| | - Jari Koistinaho
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
- Neuroscience Center University of Helsinki Helsinki Finland
| | - Katja M. Kanninen
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
| | - Minna U. Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
| | - Rosalba Giugno
- Department of Computer Science University of Verona Verona Italy
| | | | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences University of Eastern Finland Kuopio Finland
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24
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Pai S, Weber P, Isserlin R, Kaka H, Hui S, Shah MA, Giudice L, Giugno R, Nøhr AK, Baumbach J, Bader GD. netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. F1000Res 2020; 9:1239. [PMID: 33628435 PMCID: PMC7883323 DOI: 10.12688/f1000research.26429.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 12/15/2022] Open
Abstract
Patient classification based on clinical and genomic data will further the goal of precision medicine. Interpretability is of particular relevance for models based on genomic data, where sample sizes are relatively small (in the hundreds), increasing overfitting risk netDx is a machine learning method to integrate multi-modal patient data and build a patient classifier. Patient data are converted into networks of patient similarity, which is intuitive to clinicians who also use patient similarity for medical diagnosis. Features passing selection are integrated, and new patients are assigned to the class with the greatest profile similarity. netDx has excellent performance, outperforming most machine-learning methods in binary cancer survival prediction. It handles missing data – a common problem in real-world data – without requiring imputation. netDx also has excellent interpretability, with native support to group genes into pathways for mechanistic insight into predictive features. The netDx Bioconductor package provides multiple workflows for users to build custom patient classifiers. It provides turnkey functions for one-step predictor generation from multi-modal data, including feature selection over multiple train/test data splits. Workflows offer versatility with custom feature design, choice of similarity metric; speed is improved by parallel execution. Built-in functions and examples allow users to compute model performance metrics such as AUROC, AUPR, and accuracy. netDx uses RCy3 to visualize top-scoring pathways and the final integrated patient network in Cytoscape. Advanced users can build more complex predictor designs with functional building blocks used in the default design. Finally, the netDx Bioconductor package provides a novel workflow for pathway-based patient classification from sparse genetic data.
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Affiliation(s)
- Shraddha Pai
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Philipp Weber
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Ruth Isserlin
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Hussam Kaka
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Shirley Hui
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | | | - Luca Giudice
- Department of Computer Science, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Anne Krogh Nøhr
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,H. Lundbeck A/S, Copenhagen, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.,TUM School of Life Sciences Wiehenstephan, Technical University of Munich, Munich, Germany
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,The Lunenfeld-Tanenbaum Research Institute, Mount Sinal Hospital, Toronto, Canada
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25
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Bister N, Pistono C, Huremagic B, Jolkkonen J, Giugno R, Malm T. Hypoxia and extracellular vesicles: A review on methods, vesicular cargo and functions. J Extracell Vesicles 2020; 10:e12002. [PMID: 33304471 PMCID: PMC7710128 DOI: 10.1002/jev2.12002] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [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: 06/04/2020] [Revised: 09/14/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022] Open
Abstract
Hypoxia is an essential hallmark of several serious diseases such as cardiovascular and metabolic disorders and cancer. A decline in the tissue oxygen level induces hypoxic responses in cells which strive to adapt to the changed conditions. A failure to adapt to prolonged or severe hypoxia can trigger cell death. While some cell types, such as neurons, are highly vulnerable to hypoxia, cancer cells take advantage of a hypoxic environment to undergo tumour growth, angiogenesis and metastasis. Hypoxia-induced processes trigger complex intercellular communication and there are now indications that extracellular vesicles (EVs) play a fundamental role in these processes. Recent developments in EV isolation and characterization methodology have increased the awareness of the importance of EV purity in functional and cargo studies. Cell death, a hallmark of severe hypoxia, is a known source of intracellular contaminants in isolated EVs. In this review, methodological aspects of studies investigating hypoxia-induced EVs are critically evaluated. Key concerns and gaps in the current knowledge are highlighted and future directions for studies are set. To accelerate and advance research, an in-depth analysis of the functions and cargo of hypoxic EVs, compared to normoxic EVs, is provided with the focus on the altered microRNA contents of the EVs.
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Affiliation(s)
- Nea Bister
- A.I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Cristiana Pistono
- A.I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Benjamin Huremagic
- Department of Human GeneticsKU LeuvenLeuvenBelgium
- Department of Computer ScienceUniversity of VeronaVeronaItaly
| | - Jukka Jolkkonen
- A.I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
- Department of NeurologyUniversity of Eastern FinlandInstitute of Clinical MedicineKuopioFinland
| | - Rosalba Giugno
- Department of Computer ScienceUniversity of VeronaVeronaItaly
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
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26
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Mantovani E, Zucchella C, Bottiroli S, Federico A, Giugno R, Sandrini G, Chiamulera C, Tamburin S. Telemedicine and Virtual Reality for Cognitive Rehabilitation: A Roadmap for the COVID-19 Pandemic. Front Neurol 2020; 11:926. [PMID: 33041963 PMCID: PMC7522345 DOI: 10.3389/fneur.2020.00926] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [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: 06/05/2020] [Accepted: 07/17/2020] [Indexed: 12/26/2022] Open
Abstract
The current COVID-19 pandemic presents unprecedented new challenges to public health and medical care delivery. To control viral transmission, social distancing measures have been implemented all over the world, interrupting the access to routine medical care for many individuals with neurological diseases. Cognitive disorders are common in many neurological conditions, e.g., stroke, traumatic brain injury, Alzheimer's disease, and other types of dementia, Parkinson's disease and parkinsonian syndromes, and multiple sclerosis, and should be addressed by cognitive rehabilitation interventions. To be effective, cognitive rehabilitation programs must be intensive and prolonged over time; however, the current virus containment measures are hampering their implementation. Moreover, the reduced access to cognitive rehabilitation might worsen the relationship between the patient and the healthcare professional. Urgent measures to address issues connected to COVID-19 pandemic are, therefore, needed. Remote communication technologies are increasingly regarded as potential effective options to support health care interventions, including neurorehabilitation and cognitive rehabilitation. Among them, telemedicine, virtual reality, augmented reality, and serious games could be in the forefront of these efforts. We will briefly review current evidence-based recommendations on the efficacy of cognitive rehabilitation and offer a perspective on the role of tele- and virtual rehabilitation to achieve adequate cognitive stimulation in the era of social distancing related to COVID-19 pandemic. In particular, we will discuss issues related to their diffusion and propose a roadmap to address them. Methodological and technological improvements might lead to a paradigm shift to promote the delivery of cognitive rehabilitation to people with reduced mobility and in remote regions.
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Affiliation(s)
- Elisa Mantovani
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Chiara Zucchella
- Section of Neurology, Department of Neurosciences, Verona University Hospital, Verona, Italy
| | - Sara Bottiroli
- Giustino Fortunato University, Benevento, Italy.,IRCCS Mondino Foundation, Pavia, Italy
| | - Angela Federico
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Giorgio Sandrini
- IRCCS Mondino Foundation, Pavia, Italy.,Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Cristiano Chiamulera
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Stefano Tamburin
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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Bonnici V, Maresi E, Giugno R. Challenges in gene-oriented approaches for pangenome content discovery. Brief Bioinform 2020; 22:5901976. [PMID: 32893299 DOI: 10.1093/bib/bbaa198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/14/2020] [Accepted: 08/04/2020] [Indexed: 01/17/2023] Open
Abstract
Given a group of genomes, represented as the sets of genes that belong to them, the discovery of the pangenomic content is based on the search of genetic homology among the genes for clustering them into families. Thus, pangenomic analyses investigate the membership of the families to the given genomes. This approach is referred to as the gene-oriented approach in contrast to other definitions of the problem that takes into account different genomic features. In the past years, several tools have been developed to discover and analyse pangenomic contents. Because of the hardness of the problem, each tool applies a different strategy for discovering the pangenomic content. This results in a differentiation of the performance of each tool that depends on the composition of the input genomes. This review reports the main analysis instruments provided by the current state of the art tools for the discovery of pangenomic contents. Moreover, unlike previous works, the presented study compares pangenomic tools from a methodological perspective, analysing the causes that lead a given methodology to outperform other tools. The analysis is performed by taking into account different bacterial populations, which are synthetically generated by changing evolutionary parameters. The benchmarks used to compare the pangenomic tools, in addition to the computational pipeline developed for this purpose, are available at https://github.com/InfOmics/pangenes-review. Contact: V. Bonnici, R. Giugno Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.
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Affiliation(s)
| | - Emiliano Maresi
- The Microsoft Research, University of Trento Centre for Computational and Systems Biology
| | - Rosalba Giugno
- Computer Science and Bioinformatics, referent of the Master Degree in Medical Bioinformatics
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28
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Kolosowska N, Gotkiewicz M, Dhungana H, Giudice L, Giugno R, Box D, Huuskonen MT, Korhonen P, Scoyni F, Kanninen KM, Ylä-Herttuala S, Turunen TA, Turunen MP, Koistinaho J, Malm T. Intracerebral overexpression of miR-669c is protective in mouse ischemic stroke model by targeting MyD88 and inducing alternative microglial/macrophage activation. J Neuroinflammation 2020; 17:194. [PMID: 32560730 PMCID: PMC7304130 DOI: 10.1186/s12974-020-01870-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 10/30/2019] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
Background Ischemic stroke is a devastating disease without a cure. The available treatments for ischemic stroke, thrombolysis by tissue plasminogen activator, and thrombectomy are suitable only to a fraction of patients and thus novel therapeutic approaches are urgently needed. The neuroinflammatory responses elicited secondary to the ischemic attack further aggravate the stroke-induced neuronal damage. It has been demonstrated that these responses are regulated at the level of non-coding RNAs, especially miRNAs. Methods We utilized lentiviral vectors to overexpress miR-669c in BV2 microglial cells in order to modulate their polarization. To detect whether the modulation of microglial activation by miR-669c provides protection in a mouse model of transient focal ischemic stroke, miR-669c overexpression was driven by a lentiviral vector injected into the striatum prior to induction of ischemic stroke. Results Here, we demonstrate that miR-669c-3p, a member of chromosome 2 miRNA cluster (C2MC), is induced upon hypoxic and excitotoxic conditions in vitro and in two different in vivo models of stroke. Rather than directly regulating the neuronal survival in vitro, miR-669c is capable of attenuating the microglial proinflammatory activation in vitro and inducing the expression of microglial alternative activation markers arginase 1 (Arg1), chitinase-like 3 (Ym1), and peroxisome proliferator-activated receptor gamma (PPAR-γ). Intracerebral overexpression of miR-669c significantly decreased the ischemia-induced cell death and ameliorated the stroke-induced neurological deficits both at 1 and 3 days post injury (dpi). Albeit miR-669c overexpression failed to alter the overall Iba1 protein immunoreactivity, it significantly elevated Arg1 levels in the ischemic brain and increased colocalization of Arg1 and Iba1. Moreover, miR-669c overexpression under cerebral ischemia influenced several morphological characteristics of Iba1 positive cells. We further demonstrate the myeloid differentiation primary response gene 88 (MyD88) transcript as a direct target for miR-669c-3p in vitro and show reduced levels of MyD88 in miR-669c overexpressing ischemic brains in vivo. Conclusions Collectively, our data provide the evidence that miR-669c-3p is protective in a mouse model of ischemic stroke through enhancement of the alternative microglial/macrophage activation and inhibition of MyD88 signaling. Our results accentuate the importance of controlling miRNA-regulated responses for the therapeutic benefit in conditions of stroke and neuroinflammation.
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Affiliation(s)
- Natalia Kolosowska
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Maria Gotkiewicz
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Hiramani Dhungana
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Luca Giudice
- Department of Computer Science, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Daphne Box
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Mikko T Huuskonen
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Paula Korhonen
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Flavia Scoyni
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Katja M Kanninen
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Tiia A Turunen
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Mikko P Turunen
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Jari Koistinaho
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland.,Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Tarja Malm
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, P.O. Box 1627, FI-70211, Kuopio, Finland.
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Cancellieri S, Canver MC, Bombieri N, Giugno R, Pinello L. CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing. Bioinformatics 2020; 36:2001-2008. [PMID: 31764961 PMCID: PMC7141852 DOI: 10.1093/bioinformatics/btz867] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 11/16/2019] [Accepted: 11/21/2019] [Indexed: 12/26/2022] Open
Abstract
MOTIVATION Clustered regularly interspaced short palindromic repeats (CRISPR) technologies allow for facile genomic modification in a site-specific manner. A key step in this process is the in silico design of single guide RNAs to efficiently and specifically target a site of interest. To this end, it is necessary to enumerate all potential off-target sites within a given genome that could be inadvertently altered by nuclease-mediated cleavage. Currently available software for this task is limited by computational efficiency, variant support or annotation, and assessment of the functional impact of potential off-target effects. RESULTS To overcome these limitations, we have developed CRISPRitz, a suite of software tools to support the design and analysis of CRISPR/CRISPR-associated (Cas) experiments. Using efficient data structures combined with parallel computation, we offer a rapid, reliable, and exhaustive search mechanism to enumerate a comprehensive list of putative off-target sites. As proof-of-principle, we performed a head-to-head comparison with other available tools on several datasets. This analysis highlighted the unique features and superior computational performance of CRISPRitz including support for genomic searching with DNA/RNA bulges and mismatches of arbitrary size as specified by the user as well as consideration of genetic variants (variant-aware). In addition, graphical reports are offered for coding and non-coding regions that annotate the potential impact of putative off-target sites that lie within regions of functional genomic annotation (e.g. insulator and chromatin accessible sites from the ENCyclopedia Of DNA Elements [ENCODE] project). AVAILABILITY AND IMPLEMENTATION The software is freely available at: https://github.com/pinellolab/CRISPRitzhttps://github.com/InfOmics/CRISPRitz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Matthew C Canver
- Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicola Bombieri
- Computer Science Department, University of Verona, Verona 37134, Italy
| | - Rosalba Giugno
- Computer Science Department, University of Verona, Verona 37134, Italy
| | - Luca Pinello
- Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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30
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Giannuzzi D, Giudice L, Marconato L, Ferraresso S, Giugno R, Bertoni F, Aresu L. Integrated analysis of transcriptome, methylome and copy number aberrations data of marginal zone lymphoma and follicular lymphoma in dog. Vet Comp Oncol 2020; 18:645-655. [PMID: 32154977 DOI: 10.1111/vco.12588] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 07/10/2019] [Revised: 02/10/2020] [Accepted: 03/05/2020] [Indexed: 12/17/2022]
Abstract
Marginal zone lymphoma (MZL) and follicular lymphoma (FL) are classified as indolent B-cell lymphomas in dogs. Aside from the clinical and histopathological similarities with the human counterpart, the molecular pathogenesis remains unclear. We integrated transcriptome, genome-wide DNA methylation and copy number aberration analysis to provide insights on the pathogenesis of canine MZL (n = 5) and FL (n = 7), also comparing them with diffuse large B-cell lymphoma (DLBCL). Transcriptome profiling highlighted the presence of similar biological processes affecting both histotypes, including BCR and TLR signalling pathways. However, FLs showed an enrichment of E2F targets, whereas MZLs were characterized by MYC-driven transcriptional activation signatures. FLs showed a distinctive loss on chr1 containing CEACAM23 and 24, conversely MZLs presented multiple recurrent gains on chr13, where MYC is located. The distribution of methylation peaks was similar between the two histotypes. Integrating data from the three omics, FLs resulted clearly separated from MZLs and DLBCL dataset. MZLs showed the enrichment of FoxM1 network and TLR associated TICAM1-dependent IRFs activation pathway. However, no specific signatures differentiated MZLs from DLBCLs. In conclusion, our study presents the first comprehensive analysis of molecular and epigenetic pathogenesis of canine FL and MZL.
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Affiliation(s)
- Diana Giannuzzi
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
| | - Luca Giudice
- Department of Computer Science, University of Verona, Verona, Italy
| | - Laura Marconato
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Francesco Bertoni
- Università della Svizzera italiana (USI), Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | - Luca Aresu
- Department of Veterinary Science, University of Turin, Turin, Italy
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31
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Cascione L, Giudice L, Ferraresso S, Marconato L, Giannuzzi D, Napoli S, Bertoni F, Giugno R, Aresu L. Long Non-Coding RNAs as Molecular Signatures for Canine B-Cell Lymphoma Characterization. Noncoding RNA 2019; 5:ncrna5030047. [PMID: 31546795 PMCID: PMC6789837 DOI: 10.3390/ncrna5030047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 08/01/2019] [Revised: 09/06/2019] [Accepted: 09/16/2019] [Indexed: 02/08/2023] Open
Abstract
Background: Diffuse large B-cell lymphoma (DLBCL), marginal zone lymphoma (MZL) and follicular lymphoma (FL) are the most common B-cell lymphomas (BCL) in dogs. Recent investigations have demonstrated overlaps of these histotypes with the human counterparts, including clinical presentation, biologic behavior, tumor genetics, and treatment response. The molecular mechanisms that underlie canine BCL are still unknown and new studies to improve diagnosis, therapy, and the utilization of canine species as spontaneous animal tumor models are undeniably needed. Recent work using human DLBCL transcriptomes has suggested that long non-coding RNAs (lncRNAs) play a key role in lymphoma pathogenesis and pinpointed a restricted number of lncRNAs as potential targets for further studies. Results: To expand the knowledge of non-coding molecules involved in canine BCL, we used transcriptomes obtained from a cohort of 62 dogs with newly-diagnosed multicentric DLBCL, MZL and FL that had undergone complete staging work-up and were treated with chemotherapy or chemo-immunotherapy. We developed a customized R pipeline performing a transcriptome assembly by multiple algorithms to uncover novel lncRNAs, and delineate genome-wide expression of unannotated and annotated lncRNAs. Our pipeline also included a new package for high performance system biology analysis, which detects high-scoring network biological neighborhoods to identify functional modules. Moreover, our customized pipeline quantified the expression of novel and annotated lncRNAs, allowing us to subtype DLBCLs into two main groups. The DLBCL subtypes showed statistically different survivals, indicating the potential use of lncRNAs as prognostic biomarkers in future studies. Conclusions: In this manuscript, we describe the methodology used to identify lncRNAs that differentiate B-cell lymphoma subtypes and we interpreted the biological and clinical values of the results. We inferred the potential functions of lncRNAs to obtain a comprehensive and integrative insight that highlights their impact in this neoplasm.
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Affiliation(s)
- Luciano Cascione
- Institute of Oncology Research, Universita' della Svizzera Italiana, 6500 Bellinzona, Switzerland.
- Swiss Institute of Bioinformatics, 1000 Lausanne, Switzerland.
| | - Luca Giudice
- Department of Computer Science, University of Verona, 37100 Verona, Italy.
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, 35100 Padova, Italy.
| | - Laura Marconato
- Centro Oncologico Veterinario, 40037 Sasso Marconi BO, Italy.
| | - Diana Giannuzzi
- Department of Comparative Biomedicine and Food Science, University of Padova, 35100 Padova, Italy.
| | - Sara Napoli
- Institute of Oncology Research, Universita' della Svizzera Italiana, 6500 Bellinzona, Switzerland.
| | - Francesco Bertoni
- Institute of Oncology Research, Universita' della Svizzera Italiana, 6500 Bellinzona, Switzerland.
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, 37100 Verona, Italy.
| | - Luca Aresu
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, Italy.
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32
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Trovato R, Fiore A, Sartori S, Canè S, Giugno R, Cascione L, Paiella S, Salvia R, De Sanctis F, Poffe O, Anselmi C, Hofer F, Sartoris S, Piro G, Carbone C, Corbo V, Lawlor R, Solito S, Pinton L, Mandruzzato S, Bassi C, Scarpa A, Bronte V, Ugel S. Immunosuppression by monocytic myeloid-derived suppressor cells in patients with pancreatic ductal carcinoma is orchestrated by STAT3. J Immunother Cancer 2019; 7:255. [PMID: 31533831 PMCID: PMC6751612 DOI: 10.1186/s40425-019-0734-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [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: 06/12/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is a highly devastating disease with an overall 5-year survival rate of less than 8%. New evidence indicates that PDAC cells release pro-inflammatory metabolites that induce a marked alteration of normal hematopoiesis, favoring the expansion and accumulation of myeloid-derived suppressor cells (MDSCs). We report here that PDAC patients show increased levels of both circulating and tumor-infiltrating MDSC-like cells. Methods The frequency of MDSC subsets in the peripheral blood was determined by flow cytometry in three independent cohorts of PDAC patients (total analyzed patients, n = 117). Frequency of circulating MDSCs was correlated with overall survival of PDAC patients. We also analyzed the frequency of tumor-infiltrating MDSC and the immune landscape in fresh biopsies. Purified myeloid cell subsets were tested in vitro for their T-cell suppressive capacity. Results Correlation with clinical data revealed that MDSC frequency was significantly associated with a shorter patients’ overall survival and metastatic disease. However, the immunosuppressive activity of purified MDSCs was detectable only in some patients and mainly limited to the monocytic subset. A transcriptome analysis of the immunosuppressive M-MDSCs highlighted a distinct gene signature in which STAT3 was crucial for monocyte re-programming. Suppressive M-MDSCs can be characterized as circulating STAT3/arginase1-expressing CD14+ cells. Conclusion MDSC analysis aids in defining the immune landscape of PDAC patients for a more appropriate diagnosis, stratification and treatment.
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Affiliation(s)
- Rosalinda Trovato
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Alessandra Fiore
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy.,Present Address: Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sara Sartori
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Stefania Canè
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | | | - Salvatore Paiella
- General and Pancreatic Surgery, Pancreas Institute, University of Verona, Verona, Italy
| | - Roberto Salvia
- General and Pancreatic Surgery, Pancreas Institute, University of Verona, Verona, Italy
| | - Francesco De Sanctis
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Ornella Poffe
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Cristina Anselmi
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Francesca Hofer
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Silvia Sartoris
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Geny Piro
- Medical Oncology, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Rome, Italy.,Faculty of Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Carmine Carbone
- Medical Oncology, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Rome, Italy.,Faculty of Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Vincenzo Corbo
- Department of Department of Diagnostic and Public Health, University of Verona, Verona, Italy.,ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Rita Lawlor
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Samantha Solito
- Department of Surgery, Oncology and Gastroenterology, Section of Oncology and Immunology, University of Padova, Padova, Italy.,Present Address: Centro Piattaforme Tecnologiche (CPT), University of Verona, Verona, Italy
| | - Laura Pinton
- Department of Surgery, Oncology and Gastroenterology, Section of Oncology and Immunology, University of Padova, Padova, Italy
| | - Susanna Mandruzzato
- Department of Surgery, Oncology and Gastroenterology, Section of Oncology and Immunology, University of Padova, Padova, Italy.,Istituto Oncologico Veneto IOV-IRCCS, Padova, Italy
| | - Claudio Bassi
- General and Pancreatic Surgery, Pancreas Institute, University of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Department of Diagnostic and Public Health, University of Verona, Verona, Italy.,ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Vincenzo Bronte
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy.
| | - Stefano Ugel
- University Hospital and Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
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33
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Konttinen H, Cabral-da-Silva MEC, Ohtonen S, Wojciechowski S, Shakirzyanova A, Caligola S, Giugno R, Ishchenko Y, Hernández D, Fazaludeen MF, Eamen S, Budia MG, Fagerlund I, Scoyni F, Korhonen P, Huber N, Haapasalo A, Hewitt AW, Vickers J, Smith GC, Oksanen M, Graff C, Kanninen KM, Lehtonen S, Propson N, Schwartz MP, Pébay A, Koistinaho J, Ooi L, Malm T. PSEN1ΔE9, APPswe, and APOE4 Confer Disparate Phenotypes in Human iPSC-Derived Microglia. Stem Cell Reports 2019; 13:669-683. [PMID: 31522977 PMCID: PMC6829767 DOI: 10.1016/j.stemcr.2019.08.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [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: 04/15/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/20/2022] Open
Abstract
Here we elucidate the effect of Alzheimer disease (AD)-predisposing genetic backgrounds, APOE4, PSEN1ΔE9, and APPswe, on functionality of human microglia-like cells (iMGLs). We present a physiologically relevant high-yield protocol for producing iMGLs from induced pluripotent stem cells. Differentiation is directed with small molecules through primitive erythromyeloid progenitors to re-create microglial ontogeny from yolk sac. The iMGLs express microglial signature genes and respond to ADP with intracellular Ca2+ release distinguishing them from macrophages. Using 16 iPSC lines from healthy donors, AD patients and isogenic controls, we reveal that the APOE4 genotype has a profound impact on several aspects of microglial functionality, whereas PSEN1ΔE9 and APPswe mutations trigger minor alterations. The APOE4 genotype impairs phagocytosis, migration, and metabolic activity of iMGLs but exacerbates their cytokine secretion. This indicates that APOE4 iMGLs are fundamentally unable to mount normal microglial functionality in AD. APOE4 genotype has a profound impact on several functions of microglia-like cells Inflammatory responses are aggravated in cells with APOE4 genotype Metabolism, phagocytosis, and migration are decreased in APOE4 microglia-like cells Familial mutations APPswe and PSEN1ΔE9 have only minor effects on functionality
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Affiliation(s)
- Henna Konttinen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Mauricio E Castro Cabral-da-Silva
- School of Chemistry and Molecular Bioscience, Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Sohvi Ohtonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Sara Wojciechowski
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Anastasia Shakirzyanova
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Simone Caligola
- Department of Computer Science, University of Verona, Verona 37134, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona 37134, Italy
| | - Yevheniia Ishchenko
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Damián Hernández
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, VIC 3002, Australia; Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia; Department of Anatomy and Neuroscience, the University of Melbourne, Melbourne, VIC 3002, Australia
| | | | - Shaila Eamen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Mireia Gómez Budia
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Ilkka Fagerlund
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Flavia Scoyni
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Paula Korhonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Nadine Huber
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Annakaisa Haapasalo
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, VIC 3002, Australia; Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia; School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, VIC 7005, Australia
| | - James Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7000, Australia
| | - Grady C Smith
- School of Chemistry and Molecular Bioscience, Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Minna Oksanen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Caroline Graff
- Department NVS, Division of Neurogeriatrics, Karolinka Institutet, Stockholm 17176, Sweden; Theme Aging, Genetics Unit, Karolinska University Hospital-Solna, Stockholm 17176, Sweden
| | - Katja M Kanninen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Sarka Lehtonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Nicholas Propson
- Department of Molecular and Cell Biology and the Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael P Schwartz
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alice Pébay
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, VIC 3002, Australia; Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia; Department of Anatomy and Neuroscience, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Jari Koistinaho
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland; Neuroscience Center, University of Helsinki, Helsinki 00014, Finland
| | - Lezanne Ooi
- School of Chemistry and Molecular Bioscience, Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Tarja Malm
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland.
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Russo F, Di Bella S, Vannini F, Berti G, Scoyni F, Cook HV, Santos A, Nigita G, Bonnici V, Laganà A, Geraci F, Pulvirenti A, Giugno R, De Masi F, Belling K, Jensen LJ, Brunak S, Pellegrini M, Ferro A. miRandola 2017: a curated knowledge base of non-invasive biomarkers. Nucleic Acids Res 2019; 46:D354-D359. [PMID: 29036351 PMCID: PMC5753291 DOI: 10.1093/nar/gkx854] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [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: 07/06/2017] [Accepted: 09/13/2017] [Indexed: 12/13/2022] Open
Abstract
miRandola (http://mirandola.iit.cnr.it/) is a database of extracellular non-coding RNAs (ncRNAs) that was initially published in 2012, foreseeing the relevance of ncRNAs as non-invasive biomarkers. An increasing amount of experimental evidence shows that ncRNAs are frequently dysregulated in diseases. Further, ncRNAs have been discovered in different extracellular forms, such as exosomes, which circulate in human body fluids. Thus, miRandola 2017 is an effort to update and collect the accumulating information on extracellular ncRNAs that is spread across scientific publications and different databases. Data are manually curated from 314 articles that describe miRNAs, long non-coding RNAs and circular RNAs. Fourteen organisms are now included in the database, and associations of ncRNAs with 25 drugs, 47 sample types and 197 diseases. miRandola also classifies extracellular RNAs based on their extracellular form: Argonaute2 protein, exosome, microvesicle, microparticle, membrane vesicle, high density lipoprotein and circulating. We also implemented a new web interface to improve the user experience.
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Affiliation(s)
- Francesco Russo
- Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | | | - Federica Vannini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, 56127, Italy
| | - Gabriele Berti
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, 56127, Italy
| | - Flavia Scoyni
- University of Eastern Finland, Kuopio, 72010, Finland
| | - Helen V Cook
- Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Alberto Santos
- Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark.,Clinical Proteomics, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, OH 43210, USA
| | - Vincenzo Bonnici
- Department of Computer Science, University of Verona, Verona, 37134, Italy
| | - Alessandro Laganà
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Filippo Geraci
- Institute of Informatics and Telematics (IIT), National Research Council (CNR), Pisa, 56124, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, Catania, 95125, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, 37134, Italy
| | - Federico De Masi
- Department of Bio and Health Informatics, DTU Bioinformatics, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Kirstine Belling
- Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Lars J Jensen
- Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Søren Brunak
- Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Marco Pellegrini
- Institute of Informatics and Telematics (IIT), National Research Council (CNR), Pisa, 56124, Italy
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, Catania, 95125, Italy
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Romano P, Céol A, Dräger A, Fiannaca A, Giugno R, La Rosa M, Milanesi L, Pfeffer U, Rizzo R, Shin SY, Xia J, Urso A. The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes. BMC Bioinformatics 2019; 20:125. [PMID: 30999855 PMCID: PMC6472292 DOI: 10.1186/s12859-019-2681-0] [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] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was "Methods, tools and platforms for Personalised Medicine in the Big Data Era", but the traditional topics of the meeting series were also included in the event. About 40 scientific contributions were presented, including four keynote lectures, five guest lectures, and many oral communications and posters. Also, three tutorials were organised before and after the workshop. Full papers from some of the best works presented in Palermo were submitted for this Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been accepted for publication in this Supplement, for a complete presentation of the outcomes of the meeting.
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Affiliation(s)
- Paolo Romano
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genova, I-16132 Italy
| | - Arnaud Céol
- European Institute of Oncology IRCCS, Milan, 20141 Italy
| | - Andreas Dräger
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Center for Bioinformatics Tübingen (ZBIT), Tübingen, 72074 Germany
- Department of Computer Science, University of Tübingen, Tübingen, 72074 Germany
| | - Antonino Fiannaca
- ICAR-CNR, Institute for high performance computing and networking, National Research Council of Italy, Palermo, 90146 Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, 37134 Italy
| | - Massimo La Rosa
- ICAR-CNR, Institute for high performance computing and networking, National Research Council of Italy, Palermo, 90146 Italy
| | - Luciano Milanesi
- ITB-CNR, Institute of biomedical technologies, National Research Council of Italy, Segrate (MI), 20090 Italy
| | - Ulrich Pfeffer
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genova, I-16132 Italy
| | - Riccardo Rizzo
- ICAR-CNR, Institute for high performance computing and networking, National Research Council of Italy, Palermo, 90146 Italy
| | - Soo-Yong Shin
- Department of Digital Health, SAIHST, Sungkyunkwan University, Seoul, 03063 South Korea
| | - Junfeng Xia
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601 China
| | - Alfonso Urso
- ICAR-CNR, Institute for high performance computing and networking, National Research Council of Italy, Palermo, 90146 Italy
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Adamo A, Brandi J, Caligola S, Delfino P, Bazzoni R, Carusone R, Cecconi D, Giugno R, Manfredi M, Robotti E, Marengo E, Bassi G, Takam Kamga P, Dal Collo G, Gatti A, Mercuri A, Arigoni M, Olivero M, Calogero RA, Krampera M. Extracellular Vesicles Mediate Mesenchymal Stromal Cell-Dependent Regulation of B Cell PI3K-AKT Signaling Pathway and Actin Cytoskeleton. Front Immunol 2019; 10:446. [PMID: 30915084 PMCID: PMC6423067 DOI: 10.3389/fimmu.2019.00446] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [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: 11/29/2018] [Accepted: 02/19/2019] [Indexed: 12/11/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) are adult, multipotent cells of mesodermal origin representing the progenitors of all stromal tissues. MSCs possess significant and broad immunomodulatory functions affecting both adaptive and innate immune responses once MSCs are primed by the inflammatory microenvironment. Recently, the role of extracellular vesicles (EVs) in mediating the therapeutic effects of MSCs has been recognized. Nevertheless, the molecular mechanisms responsible for the immunomodulatory properties of MSC-derived EVs (MSC-EVs) are still poorly characterized. Therefore, we carried out a molecular characterization of MSC-EV content by high-throughput approaches. We analyzed miRNA and protein expression profile in cellular and vesicular compartments both in normal and inflammatory conditions. We found several proteins and miRNAs involved in immunological processes, such as MOES, LG3BP, PTX3, and S10A6 proteins, miR-155-5p, and miR-497-5p. Different in silico approaches were also performed to correlate miRNA and protein expression profile and then to evaluate the putative molecules or pathways involved in immunoregulatory properties mediated by MSC-EVs. PI3K-AKT signaling pathway and the regulation of actin cytoskeleton were identified and functionally validated in vitro as key mediators of MSC/B cell communication mediated by MSC-EVs. In conclusion, we identified different molecules and pathways responsible for immunoregulatory properties mediated by MSC-EVs, thus identifying novel therapeutic targets as safer and more useful alternatives to cell or EV-based therapeutic approaches.
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Affiliation(s)
- Annalisa Adamo
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Jessica Brandi
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Simone Caligola
- Department of Computer Science, University of Verona, Verona, Italy
| | - Pietro Delfino
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Riccardo Bazzoni
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Roberta Carusone
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Daniela Cecconi
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Marcello Manfredi
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), Novara, Italy
| | - Elisa Robotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), Novara, Italy
| | - Giulio Bassi
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Paul Takam Kamga
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Giada Dal Collo
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Alessandro Gatti
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Angela Mercuri
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | | | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - Mauro Krampera
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
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Alongi P, Sardina DS, Coppola R, Scalisi S, Puglisi V, Arnone A, Raimondo GD, Munerati E, Alaimo V, Midiri F, Russo G, Stefano A, Giugno R, Piccoli T, Midiri M, Grimaldi LME. 18F-Florbetaben PET/CT to Assess Alzheimer's Disease: A new Analysis Method for Regional Amyloid Quantification. J Neuroimaging 2019; 29:383-393. [PMID: 30714241 DOI: 10.1111/jon.12601] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND AND PURPOSE While AD can be definitively confirmed by postmortem histopathologic examination, in vivo imaging may improve the clinician's ability to identify AD at the earliest stage. The aim of the study was to test the performance of amyloid PET using new processing imaging algorithm for more precise diagnosis of AD. METHODS Amyloid PET results using a new processing imaging algorithm (MRI-Less and AAL Atlas) were correlated with clinical, cognitive status, CSF analysis, and other imaging. The regional SUVR using the white matter of cerebellum as reference region and scores from clinical and cognitive tests were used to create ROC curves. Leave-one-out cross-validation was carried out to validate the results. RESULTS Forty-four consecutive patients with clinical evidence of dementia, were retrospectively evaluated. Amyloid PET scan was positive in 26/44 patients with dementia. After integration with 18F-FDG PET, clinical data and CSF protein levels, 22 of them were classified as AD, the remaining 4 as vascular or frontotemporal dementia. Amyloid and FDG PET, CDR 1, CSF Tau, and p-tau levels showed the best true positive and true negative rates (amyloid PET: AUC = .85, sensitivity .91, specificity .79). A SUVR value of 1.006 in the inferior frontal cortex and of 1.03 in the precuneus region was the best cutoff SUVR value and showed a good correlation with the diagnosis of AD. Thirteen of 44 amyloid PET positive patients have been enrolled in clinical trials using antiamyloid approaches. CONCLUSIONS Amyloid PET using SPM-normalized SUVR analysis showed high predictive power for the differential diagnosis of AD.
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Affiliation(s)
- Pierpaolo Alongi
- Department of Radiological Sciences, Nuclear Medicine Service, Fondazione Istituto G. Giglio, Contrada Pietrapollastra-Pisciotto, 90015, Cefalù, Italy
| | - Davide Stefano Sardina
- Department of Mathematics and Computer Science, University of Catania, Viale Andrea Doria 6, 95125, Catania, Italy.,Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Cefalù, Italy
| | - Rosalia Coppola
- U.O.C. Neurologia, Fondazione IstitutoG. Giglio, Contrada Pietrapollastra-Pisciotto, 90015, Cefalù, Italy
| | - Salvatore Scalisi
- Department of Radiological Sciences, Nuclear Medicine Service, Fondazione Istituto G. Giglio, Contrada Pietrapollastra-Pisciotto, 90015, Cefalù, Italy
| | - Valentina Puglisi
- U.O.C. Neurologia, Fondazione IstitutoG. Giglio, Contrada Pietrapollastra-Pisciotto, 90015, Cefalù, Italy
| | | | - Giorgio Di Raimondo
- U.O.C. Neurologia, Fondazione IstitutoG. Giglio, Contrada Pietrapollastra-Pisciotto, 90015, Cefalù, Italy
| | - Elisabetta Munerati
- U.O.C. Neurologia, Fondazione IstitutoG. Giglio, Contrada Pietrapollastra-Pisciotto, 90015, Cefalù, Italy
| | - Valerio Alaimo
- Department of Radiological Sciences, Unit of Radiology, Fondazione Istituto G. Giglio, Contrada Pietrapollastra-Pisciotto, 90015, Cefalù, Italy
| | | | - Giorgio Russo
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Cefalù, Italy
| | - Alessandro Stefano
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Cefalù, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Tommaso Piccoli
- Department of Biomedicine and Clinical Neuroscience, University of Palermo, Palermo, Italy
| | - Massimo Midiri
- Department of Radiological Sciences, Nuclear Medicine Service, Fondazione Istituto G. Giglio, Contrada Pietrapollastra-Pisciotto, 90015, Cefalù, Italy
| | - Luigi M E Grimaldi
- U.O.C. Neurologia, Fondazione IstitutoG. Giglio, Contrada Pietrapollastra-Pisciotto, 90015, Cefalù, Italy
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Mensi A, Bonnici V, Caligola S, Giugno R. Construction and Analysis of miRNA Regulatory Networks. Methods Mol Biol 2019; 1970:121-167. [PMID: 30963492 DOI: 10.1007/978-1-4939-9207-2_9] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This chapter is devoted to illustrate the usage of state-of-the-art methodologies for miRNA regulatory network construction and analysis. Advantages in understanding the role of miRNAs in regulating gene expression are increasing the possibility of developing targeted therapies and drugs. This new possibility can be exploited by gaining new knowledge through analyzing interactions between a specific miRNA and a targeted gene.
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Affiliation(s)
- Antonella Mensi
- Department of Computer Science, University of Verona, Verona, Italy
| | - Vincenzo Bonnici
- Department of Computer Science, University of Verona, Verona, Italy
| | - Simone Caligola
- Department of Computer Science, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy.
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Russo G, Sardina D, Alongi P, Coppola R, Puglisi V, Stefano A, Giugno R, Grimaldi L, Scalisi S, Midiri M, Gilardi M. 79. Amyloid-PET analysis based on tissue probability maps. Phys Med 2018. [DOI: 10.1016/j.ejmp.2018.04.089] [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: 11/28/2022] Open
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Abstract
Background Pan-genome approaches afford the discovery of homology relations in a set of genomes, by determining how some gene families are distributed among a given set of genomes. The retrieval of a complete gene distribution among a class of genomes is an NP-hard problem because computational costs increase with the number of analyzed genomes, in fact, all-against-all gene comparisons are required to completely solve the problem. In presence of phylogenetically distant genomes, due to the variability introduced in gene duplication and transmission, the task of recognizing homologous genes becomes even more difficult. A challenge on this field is that of designing fast and adaptive similarity measures in order to find a suitable pan-genome structure of homology relations. Results We present PanDelos, a stand alone tool for the discovery of pan-genome contents among phylogenetic distant genomes. The methodology is based on information theory and network analysis. It is parameter-free because thresholds are automatically deduced from the context. PanDelos avoids sequence alignment by introducing a measure based on k-mer multiplicity. The k-mer length is defined according to general arguments rather than empirical considerations. Homology candidate relations are integrated into a global network and groups of homologous genes are extracted by applying a community detection algorithm. Conclusions PanDelos outperforms existing approaches, Roary and EDGAR, in terms of running times and quality content discovery. Tests were run on collections of real genomes, previously used in analogous studies, and in synthetic benchmarks that represent fully trusted golden truth. The software is available at https://github.com/GiugnoLab/PanDelos. Electronic supplementary material The online version of this article (10.1186/s12859-018-2417-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vincenzo Bonnici
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, 37134, Italy.
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, 37134, Italy
| | - Vincenzo Manca
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, 37134, Italy
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Bonnici V, Busato F, Aldegheri S, Akhmedov M, Cascione L, Carmena AA, Bertoni F, Bombieri N, Kwee I, Giugno R. Correction to: cuRnet: an R package for graph traversing on GPU. BMC Bioinformatics 2018; 19:456. [PMID: 30482173 PMCID: PMC6260727 DOI: 10.1186/s12859-018-2484-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Vincenzo Bonnici
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, Italy
| | - Federico Busato
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, Italy
| | - Stefano Aldegheri
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, Italy
| | - Murodzhon Akhmedov
- Institute of Oncology Research (IOR), Via Vincenzo Vela 6, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research (IOR), Via Vincenzo Vela 6, Bellinzona, Switzerland
| | | | - Francesco Bertoni
- Institute of Oncology Research (IOR), Via Vincenzo Vela 6, Bellinzona, Switzerland
| | - Nicola Bombieri
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, Italy
| | - Ivo Kwee
- Institute of Oncology Research (IOR), Via Vincenzo Vela 6, Bellinzona, Switzerland
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, Italy.
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Bonnici V, Busato F, Aldegheri S, Akhmedov M, Cascione L, Carmena AA, Bertoni F, Bombieri N, Kwee I, Giugno R. cuRnet: an R package for graph traversing on GPU. BMC Bioinformatics 2018; 19:356. [PMID: 30367572 PMCID: PMC6191969 DOI: 10.1186/s12859-018-2310-3] [Citation(s) in RCA: 4] [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] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND R has become the de-facto reference analysis environment in Bioinformatics. Plenty of tools are available as packages that extend the R functionality, and many of them target the analysis of biological networks. Several algorithms for graphs, which are the most adopted mathematical representation of networks, are well-known examples of applications that require high-performance computing, and for which classic sequential implementations are becoming inappropriate. In this context, parallel approaches targeting GPU architectures are becoming pervasive to deal with the execution time constraints. Although R packages for parallel execution on GPUs are already available, none of them provides graph algorithms. RESULTS This work presents cuRnet, a R package that provides a parallel implementation for GPUs of the breath-first search (BFS), the single-source shortest paths (SSSP), and the strongly connected components (SCC) algorithms. The package allows offloading computing intensive applications to GPU devices for massively parallel computation and to speed up the runtime up to one order of magnitude with respect to the standard sequential computations on CPU. We have tested cuRnet on a benchmark of large protein interaction networks and for the interpretation of high-throughput omics data thought network analysis. CONCLUSIONS cuRnet is a R package to speed up graph traversal and analysis through parallel computation on GPUs. We show the efficiency of cuRnet applied both to biological network analysis, which requires basic graph algorithms, and to complex existing procedures built upon such algorithms.
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Affiliation(s)
- Vincenzo Bonnici
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Italy, Verona, Italy
| | - Federico Busato
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Italy, Verona, Italy
| | - Stefano Aldegheri
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Italy, Verona, Italy
| | - Murodzhon Akhmedov
- Institute of Oncology Research (IOR), Via Vincenzo Vela 6, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research (IOR), Via Vincenzo Vela 6, Bellinzona, Switzerland
| | | | - Francesco Bertoni
- Institute of Oncology Research (IOR), Via Vincenzo Vela 6, Bellinzona, Switzerland
| | - Nicola Bombieri
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Italy, Verona, Italy
| | - Ivo Kwee
- Institute of Oncology Research (IOR), Via Vincenzo Vela 6, Bellinzona, Switzerland
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Italy, Verona, Italy.
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Giugno R, Manca V. Editorial: New Trends on Genome and Transcriptome Characterizations. Front Genet 2018; 9:322. [PMID: 30177950 PMCID: PMC6109641 DOI: 10.3389/fgene.2018.00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/30/2018] [Indexed: 11/25/2022] Open
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Abstract
Background The analysis of tissue-specific protein interaction networks and their functional enrichment in pathological and normal tissues provides insights on the etiology of diseases. The Pan-cancer proteomic project, in The Cancer Genome Atlas, collects protein expressions in human cancers and it is a reference resource for the functional study of cancers. However, established protocols to infer interaction networks from protein expressions are still missing. Results We have developed a methodology called Inference Network Based on iRefIndex Analysis (INBIA) to accurately correlate proteomic inferred relations to protein-protein interaction (PPI) networks. INBIA makes use of 14 network inference methods on protein expressions related to 16 cancer types. It uses as reference model the iRefIndex human PPI network. Predictions are validated through non-interacting and tissue specific PPI networks resources. The first, Negatome, takes into account likely non-interacting proteins by combining both structure properties and literature mining. The latter, TissueNet and GIANT, report experimentally verified PPIs in more than 50 human tissues. The reliability of the proposed methodology is assessed by comparing INBIA with PERA, a tool which infers protein interaction networks from Pathway Commons, by both functional and topological analysis. Conclusion Results show that INBIA is a valuable approach to predict proteomic interactions in pathological conditions starting from the current knowledge of human protein interactions. Electronic supplementary material The online version of this article (10.1186/s12859-018-2183-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Davide S Sardina
- Department of Computer Science, University of Verona, Strada le Grazie 15, Verona, 37134, Italy
| | - Giovanni Micale
- Department of Mathematics and Computer Science, University of Catania, Viale A. Doria 6, Catania, 95125, Italy
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science, Viale A. Doria 6, Catania, 95125, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science, Viale A. Doria 6, Catania, 95125, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie 15, Verona, 37134, Italy.
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Adamo A, Brandi J, Carusone R, Caligola S, Cecconi D, Giugno R, Manfredi M, Robotti E, Marengo E, Dal Collo G, Bazzoni R, Arigoni M, Calogero R, Gatti A, Takam Kamga P, Mercuri A, Krampera M. Molecular characterization of msc-derived extracellular vesicles and correlation with their immunomodulatory potential. Cytotherapy 2018. [DOI: 10.1016/j.jcyt.2018.02.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Alaimo S, Giugno R, Acunzo M, Veneziano D, Ferro A, Pulvirenti A. Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification. Oncotarget 2018; 7:54572-54582. [PMID: 27275538 PMCID: PMC5342365 DOI: 10.18632/oncotarget.9788] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 10/21/2015] [Accepted: 05/11/2016] [Indexed: 01/27/2023] Open
Abstract
Motivation Prediction of phenotypes from high-dimensional data is a crucial task in precision biology and medicine. Many technologies employ genomic biomarkers to characterize phenotypes. However, such elements are not sufficient to explain the underlying biology. To improve this, pathway analysis techniques have been proposed. Nevertheless, such methods have shown lack of accuracy in phenotypes classification. Results Here we propose a novel methodology called MITHrIL (Mirna enrIched paTHway Impact anaLysis) for the analysis of signaling pathways, which extends the work of Tarca et al., 2009. MITHrIL augments pathways with missing regulatory elements, such as microRNAs, and their interactions with genes. The method takes as input the expression values of genes and/or microRNAs and returns a list of pathways sorted according to their degree of deregulation, together with the corresponding statistical significance (p-values). Our analysis shows that MITHrIL outperforms its competitors even in the worst case. In addition, our method is able to correctly classify sets of tumor samples drawn from TCGA. Availability MITHrIL is freely available at the following URL: http://alpha.dmi.unict.it/mithril/
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Affiliation(s)
- Salvatore Alaimo
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Mario Acunzo
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Dario Veneziano
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
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Alaimo S, Marceca GP, Giugno R, Ferro A, Pulvirenti A. Current Knowledge and Computational Techniques for Grapevine Meta-Omics Analysis. Front Plant Sci 2017; 8:2241. [PMID: 29375610 PMCID: PMC5767322 DOI: 10.3389/fpls.2017.02241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 12/20/2017] [Indexed: 05/03/2023]
Abstract
Growing grapevine (Vitis vinifera) is a key contribution to the economy of many countries. Tools provided by genomics and bioinformatics did help researchers in obtaining biological knowledge about the different cultivars. Several genetic markers for common diseases were identified. Recently, the impact of microbiome has been proved to be of fundamental importance both in humans and in plants for its ability to confer protection or induce diseases. In this review we report current knowledge about grapevine microbiome, together with a description of the available computational methodologies for meta-omics analysis.
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Affiliation(s)
- Salvatore Alaimo
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Gioacchino P. Marceca
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Alfredo Ferro
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alfredo Pulvirenti
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
- *Correspondence: Alfredo Pulvirenti
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Abstract
Graphs are mathematical structures to model several biological data. Applications to analyze them require to apply solutions for the subgraph isomorphism problem, which is NP-complete. Here, we investigate the existing strategies to reduce the subgraph isomorphism algorithm running time with emphasis on the importance of the order with which the graph vertices are taken into account during the search, called variable ordering, and its incidence on the total running time of the algorithms. We focus on two recent solutions, which are based on an effective variable ordering strategy. We discuss their comparison both with the variable ordering strategies reviewed in the paper and the other algorithms present in the ICPR2014 contest on graph matching algorithms for pattern search in biological databases.
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Sardina DS, Alaimo S, Ferro A, Pulvirenti A, Giugno R. A novel computational method for inferring competing endogenous interactions. Brief Bioinform 2016; 18:1071-1081. [DOI: 10.1093/bib/bbw084] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 12/14/2022] Open
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Bonnici V, Busato F, Micale G, Bombieri N, Pulvirenti A, Giugno R. APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks. Bioinformatics 2016; 32:2159-66. [DOI: 10.1093/bioinformatics/btw223] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/10/2016] [Indexed: 02/02/2023] Open
Affiliation(s)
- Vincenzo Bonnici
- Department of Computer Science, University of Verona, Strada Le Grazie, Verona
| | - Federico Busato
- Department of Computer Science, University of Verona, Strada Le Grazie, Verona
| | - Giovanni Micale
- Department of Math and Computer Science, University of Catania, Viale a. Doria, Catania
| | - Nicola Bombieri
- Department of Computer Science, University of Verona, Strada Le Grazie, Verona
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, via Palermo, Catania
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada Le Grazie, Verona
- Department of Clinical and Experimental Medicine, University of Catania, via Palermo, Catania
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