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Padoan E, Ferraresso S, Pegolo S, Barnini C, Castagnaro M, Bargelloni L. Gene Expression Profiles of the Immuno-Transcriptome in Equine Asthma. Animals (Basel) 2022; 13:ani13010004. [PMID: 36611613 PMCID: PMC9817691 DOI: 10.3390/ani13010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Mild equine asthma (MEA) and severe equine asthma (SEA) are two of the most frequent equine airway inflammatory diseases, but knowledge about their pathogenesis is limited. The goal of this study was to investigate gene expression differences in the respiratory tract of MEA- and SEA-affected horses and their relationship with clinical signs. METHODS Clinical examination and endoscopy were performed in 8 SEA- and 10 MEA-affected horses and 7 healthy controls. Cytological and microbiological analyses of bronchoalveolar lavage (BAL) fluid were performed. Gene expression profiling of BAL fluid was performed by means of a custom oligo-DNA microarray. RESULTS In both MEA and SEA, genes involved in the genesis, length, and motility of respiratory epithelium cilia were downregulated. In MEA, a significant overexpression for genes encoding inflammatory mediators was observed. In SEA, transcripts involved in bronchoconstriction, apoptosis, and hypoxia pathways were significantly upregulated, while genes involved in the formation of the protective muco-protein film were underexpressed. The SEA group also showed enrichment of gene networks activated during human asthma. CONCLUSIONS The present study provides new insight into equine asthma pathogenesis, representing the first step in transcriptomic analysis to improve diagnostic and therapeutic approaches for this respiratory disease.
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Affiliation(s)
- Elisa Padoan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
- Correspondence: ; Tel.: +39-049-8272506
| | - Sara Pegolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
| | | | - Massimo Castagnaro
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
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2
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Bernardini I, Fabrello J, Vecchiato M, Ferraresso S, Babbucci M, Peruzza L, Rovere GD, Masiero L, Marin MG, Bargelloni L, Gambaro A, Patarnello T, Matozzo V, Milan M. Effects of environmental concentrations of the fragrance amyl salicylate on the mediterranean mussel Mytilus galloprovincialis. Environ Pollut 2022; 307:119502. [PMID: 35605833 DOI: 10.1016/j.envpol.2022.119502] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/06/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Amyl salicylate (AS) is a fragrance massively used as a personal care product and following the discharged in wastewaters may end up in the aquatic environment representing a potential threat for the ecosystem and living organisms. AS was recently detected in water of the Venice Lagoon, a vulnerable area continuously subjected to the income of anthropogenic chemicals. The lagoon is a relevant area for mollusc farming, including the Mediterranean mussels (Mytilus galloprovincialis) having an important economic and ecological role. Despite high levels of AS occurred in water of the Lagoon of Venice, no studies investigated the possible consequences of AS exposures on species inhabiting this ecosystem to date. For the first time, we applied a multidisciplinary approach to investigate the potential effects of the fragrance AS on Mediterranean mussels. To reach such a goal, bioaccumulation, cellular, biochemical, and molecular analyses (RNA-seq and microbiota characterization) were measured in mussels treated for 7 and 14 days with different AS Venice lagoon environmental levels (0.1 and 0.5 μg L-1). Despite chemical investigations suggested low AS bioaccumulation capability, cellular and molecular analyses highlighted the disruption of several key cellular processes after the prolonged exposures to the high AS concentration. Among them, potential immunotoxicity and changes in transcriptional regulation of pathways involved in energy metabolism, stress response, apoptosis and cell death regulations have been observed. Conversely, exposure to the low AS concentration demonstrated weak transcriptional changes and transient increased representation of opportunistic pathogens, as Arcobacter genus and Vibrio aestuarianus. Summarizing, this study provides the first overview on the effects of AS on one of the most widely farmed mollusk species.
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Affiliation(s)
- I Bernardini
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - J Fabrello
- Department of Biology, University of Padova, Via Bassi 58/B, 35131, Padova, Italy
| | - M Vecchiato
- Institute of Polar Sciences - National Research Council (ISP-CNR), Via Torino 155, 30172, Venezia-Mestre, Venice, Italy; Department of Environmental Sciences, Informatics and Statistics (DAIS), Ca' Foscari University of Venice, Via Torino 155, 30172, Venezia-Mestre, Venice, Italy
| | - S Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - M Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - L Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - L Masiero
- Department of Biology, University of Padova, Via Bassi 58/B, 35131, Padova, Italy
| | - M G Marin
- Department of Biology, University of Padova, Via Bassi 58/B, 35131, Padova, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - A Gambaro
- Institute of Polar Sciences - National Research Council (ISP-CNR), Via Torino 155, 30172, Venezia-Mestre, Venice, Italy; Department of Environmental Sciences, Informatics and Statistics (DAIS), Ca' Foscari University of Venice, Via Torino 155, 30172, Venezia-Mestre, Venice, Italy
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - V Matozzo
- Department of Biology, University of Padova, Via Bassi 58/B, 35131, Padova, Italy.
| | - M Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
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3
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Iannello M, Mezzelani M, Dalla Rovere G, Smits M, Patarnello T, Ciofi C, Carraro L, Boffo L, Ferraresso S, Babbucci M, Mazzariol S, Centelleghe C, Cardazzo B, Carrer C, Varagnolo M, Nardi A, Pittura L, Benedetti M, Fattorini D, Regoli F, Ghiselli F, Gorbi S, Bargelloni L, Milan M. Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam. Evol Appl 2021; 14:2864-2880. [PMID: 34950234 PMCID: PMC8674894 DOI: 10.1111/eva.13319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative approach was implemented, combining transcriptome, genetic and microbiota analyses with the evaluation of biochemical and histological profiles of the edible Manila clam Ruditapes philippinarum, as it was transplanted for 6 months from the polluted area of Porto Marghera (PM) to the clean area of Chioggia (Venice lagoon, Italy). One month post-transplantation, PM clams showed several modifications to its resident microbiota, including an overrepresentation of the opportunistic pathogen Arcobacter spp. This may be related to the upregulation of several immune genes in the PM clams, potentially representing a host response to the increased abundance of deleterious bacteria. Six months after transplantation, PM clams demonstrated a lower ability to respond to environmental/physiological stressors related to the summer season, and the hepatopancreas-associated microbiota still showed different compositions among PM and CH clams. This study confirms that different stressors have predictable effects in clams at different biological levels and demonstrates that chronic exposure to pollutants leads to long-lasting effects on the animal hologenome. In addition, no genetic differentiation between samples from the two areas was detected, confirming that PM and CH clams belong to a single population. Overall, the obtained responses were largely reversible and potentially related to phenotypic plasticity rather than genetic adaptation. The results here presented will be functional for the assessment of the environmental risk imposed by chemicals on an economically important bivalve species.
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Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Marica Mezzelani
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Morgan Smits
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Claudio Ciofi
- Department of BiologyUniversity of FlorenceSesto FiorentinoItaly
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Luciano Boffo
- Associazione “Vongola Verace di Chioggia”ChioggiaItaly
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Sandro Mazzariol
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Cinzia Centelleghe
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Claudio Carrer
- c/o Magistrato alle Acque di Venezia Ufficio Tecnico Antinquinamento Laboratorio CSMOPadovaItaly
| | | | - Alessandro Nardi
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Lucia Pittura
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Maura Benedetti
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Daniele Fattorini
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Francesco Regoli
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Stefania Gorbi
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Massimo Milan
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
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4
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Peruzza L, Pascoli F, Dalla Rovere G, Franch R, Ferraresso S, Babbucci M, Biasini L, Abbadi M, Panzarin V, Toffan A, Bargelloni L. Transcriptome analysis reveals a complex response to the RGNNV/SJNNV reassortant Nervous Necrosis Virus strain in sea bream larvae. Fish Shellfish Immunol 2021; 114:282-292. [PMID: 33971258 DOI: 10.1016/j.fsi.2021.04.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
The gilthead sea bream (Sparus aurata) is a marine fish of great importance for Mediterranean aquaculture. This species has long been considered resistant to Nervous Necrosis Virus (NNV), an RNA virus that causes massive mortalities in several farmed fish animals. However, the recent appearance of RGNNV/SJNNV reassortant strains started to pose a serious threat to sea bream hatcheries, as it is able to infect larvae and juveniles of this species. While host response to NNV has been extensively studied in adult fish, little attention has been devoted to early life history stages, which are generally the most sensitive ones. Here we report for the first time a time-course RNA-seq analysis on 21-day old fish gilthead sea bream larvae experimentally infected with a RGNNV/SJNNV strain. NNV-infected and mock-infected samples were collected at four time points (6 h, 12 h, 24 h, and 48 h post infection). Four biological replicates, each consisting of five pooled larvae, were analysed for each time point and group. A large set of genes were found to be significantly regulated, especially at early time points (6 h and 12 h), with several heat shock protein encoding transcripts being up-regulated (e.g. hspa5, dnaj4, hspa9, hsc70), while many immune genes were down-regulated (e.g. myd88 and irf5 at T06, pik3r1, stat3, jak1, il12b and il6st at T12). A gene set enrichment analysis (GSEA) identified several altered pathways/processes. For instance, the formation of peroxisomes, which are important anti-viral components as well as essential for nervous system homeostasis, and the autophagy pathway were down-regulated at 6 h and 24 h post infection (hpi). Finally, two custom "reactomes" (i.e. significant gene sets observed in other studies) were defined and used. The first reactome integrated the transcriptomic response to NNV in different fish species, while the second one included all genes found to be stimulated either by interferon (IFN) or by IFN and Chikungunya virus in zebrafish. Genes in both reactomes showed predominant up-regulation at 6hpi and 12hpi and a general down-regulation at 24hpi. Such evidence suggest a certain degree of similarity between the response of sea bream and that of other fish species to NNV, while the observed down-regulation of IFN- and viral-stimulated pathways argues for a possible interference of NNV against the host response.
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Affiliation(s)
- L Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università, 16 35020, Legnaro, PD, Italy.
| | - F Pascoli
- Division of Comparative Biomedical Sciences, OIE Reference Centre for Viral Encephalopathy and Retinopathy, Istituto Zooprofilattico Sperimentale Delle Venezie (IZSVe), Padua, Italy
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università, 16 35020, Legnaro, PD, Italy
| | - R Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università, 16 35020, Legnaro, PD, Italy
| | - S Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università, 16 35020, Legnaro, PD, Italy
| | - M Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università, 16 35020, Legnaro, PD, Italy
| | - L Biasini
- Division of Comparative Biomedical Sciences, OIE Reference Centre for Viral Encephalopathy and Retinopathy, Istituto Zooprofilattico Sperimentale Delle Venezie (IZSVe), Padua, Italy
| | - M Abbadi
- Division of Comparative Biomedical Sciences, OIE Reference Centre for Viral Encephalopathy and Retinopathy, Istituto Zooprofilattico Sperimentale Delle Venezie (IZSVe), Padua, Italy
| | - V Panzarin
- Division of Comparative Biomedical Sciences, OIE Reference Centre for Viral Encephalopathy and Retinopathy, Istituto Zooprofilattico Sperimentale Delle Venezie (IZSVe), Padua, Italy
| | - A Toffan
- Division of Comparative Biomedical Sciences, OIE Reference Centre for Viral Encephalopathy and Retinopathy, Istituto Zooprofilattico Sperimentale Delle Venezie (IZSVe), Padua, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Dell'Università, 16 35020, Legnaro, PD, Italy
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5
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Ferraresso S, Bargelloni L, Babbucci M, Cannas R, Follesa MC, Carugati L, Melis R, Cau A, Koutrakis M, Sapounidis A, Crosetti D, Patarnello T. fshr: a fish sex-determining locus shows variable incomplete penetrance across flathead grey mullet populations. iScience 2021; 24:101886. [PMID: 33354664 PMCID: PMC7744951 DOI: 10.1016/j.isci.2020.101886] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/23/2020] [Accepted: 11/25/2020] [Indexed: 12/29/2022] Open
Abstract
Whole-genome sequencing data were produced from a single flathead grey mullet female and assembled into a draft genome sequence, whereas publicly available sequence data were used to obtain a male draft sequence. Two pools, each consisting of 60 unrelated individuals, respectively, of male and female fish were analyzed using Pool-Sequencing. Mapping and analysis of Pool-Seq data against the draft genome(s) revealed >30 loci potentially associated with sex, the most promising locus of which, encoding the follicle-stimulating hormone receptor (fshr) and harboring two missense variants, was genotyped on 245 fish from four Mediterranean populations. Genotype data showed that fshr represents a previously unknown sex-determining locus, although the incomplete association pattern between fshr genotype and sex-phenotype, the variability of such pattern across different populations, and the presence of other candidate loci reveal that a greater complexity underlies sex determination in the flathead grey mullet.
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Affiliation(s)
- Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua 35020, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua 35020, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua 35020, Italy
| | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Maria Cristina Follesa
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Laura Carugati
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Riccardo Melis
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Angelo Cau
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Manos Koutrakis
- Fisheries Research Institute, Hellenic Agricultural Organisation, Nea Peramos Kavalas 640 07, Greece
| | - Argyrios Sapounidis
- Fisheries Research Institute, Hellenic Agricultural Organisation, Nea Peramos Kavalas 640 07, Greece
| | - Donatella Crosetti
- Department BIO-AMC, Institute for Environmental Protection and Research (ISPRA), Rome 00144, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua 35020, Italy
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6
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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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7
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Smits M, Enez F, Ferraresso S, Dalla Rovere G, Vetois E, Auvray JF, Genestout L, Mahla R, Arcangeli G, Paillard C, Haffray P, Bargelloni L. Potential for Genetic Improvement of Resistance to Perkinsus olseni in the Manila Clam, Ruditapes philippinarum, Using DNA Parentage Assignment and Mass Spawning. Front Vet Sci 2020; 7:579840. [PMID: 33195590 PMCID: PMC7649815 DOI: 10.3389/fvets.2020.579840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/08/2020] [Indexed: 02/05/2023] Open
Abstract
The Manila clam Ruditapes philippinarum, a major cultured shellfish species, is threatened by infection with the microparasite Perkinsus olseni, whose prevalence increases with high water temperatures. Under the current trend of climate change, the already severe effects of this parasitic infection might rapidly increase the frequency of mass mortality events. Treating infectious diseases in bivalves is notoriously problematic, therefore selective breeding for resistance represents a key strategy for mitigating the negative impact of pathogens. A crucial step in initiating selective breeding is the estimation of genetic parameters for traits of interest, which relies on the ability to record parentage and accurate phenotypes in a large number of individuals. Here, to estimate the heritability of resistance against P. olseni, a field experiment mirroring conditions in industrial clam production was set up, a genomic tool was developed for parentage assignment, and parasite load was determined through quantitative PCR. A mixed-family cohort of potentially 1,479 clam families was produced in a hatchery by mass spawning of 53 dams and 57 sires. The progenies were seeded in a commercial clam production area in the Venice lagoon, Italy, where high prevalence of P. olseni had previously been reported. Growth and parasite load were monitored every month and, after 1 year, more than 1,000 individuals were collected for DNA samples and phenotype recording. A pooled sequencing approach was carried out using DNA samples from the hatchery broodstock and from a Venice lagoon clam population, providing candidate markers used to develop a 245-SNP panel. Parentage assignment for 246 F1 individuals showed sire and dam representation were high (75 and 85%, respectively), indicating a very limited risk of inbreeding. Moderate heritability (0.23 ± 0.11-0.35 ± 0.13) was estimated for growth traits (shell length, shell weight, total weight), while parasite load showed high heritability, estimated at 0.51 ± 0.20. No significant genetic correlations were found between growth-associated traits and parasite load. Overall, the preliminary results provided by this study show high potential for selecting clams resistant to parasite load. Breeding for resistance may help limit the negative effects of climate change on clam production, as the prevalence of the parasite is predicted to increase under a future scenario of higher temperatures. Finally, the limited genetic correlation between resistance and growth suggests that breeding programs could incorporate dual selection without negative interactions.
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Affiliation(s)
- Morgan Smits
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
- Morgan Smits
| | - Florian Enez
- Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Emilie Vetois
- Société Atlantique de Mariculture (SATMAR), Gatteville-Phare, France
| | | | | | - Rachid Mahla
- Labogena, Domaine de Vilvert, Jouy en Josas, France
| | - Giuseppe Arcangeli
- National Reference Centre for Fish, Crustacean and Mollusc Pathology, Italian Health Authority and Research Organization for Animal Health and Food Safety (IZSVe), Legnaro, Italy
| | - Christine Paillard
- Laboratory of Marine Environmental Sciences (LEMAR), Institut Universitaire Européen de la Mer, Plouzané, France
| | - Pierrick Haffray
- Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
- *Correspondence: Luca Bargelloni
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8
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Brocca G, Ferraresso S, Zamboni C, Martinez-Merlo EM, Ferro S, Goldschmidt MH, Castagnaro M. Array Comparative Genomic Hybridization Analysis Reveals Significantly Enriched Pathways in Canine Oral Melanoma. Front Oncol 2019; 9:1397. [PMID: 31921654 PMCID: PMC6920211 DOI: 10.3389/fonc.2019.01397] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/26/2019] [Indexed: 12/28/2022] Open
Abstract
Human Mucosal Melanoma (hMM) is an aggressive neoplasm of neuroectodermal origin with distinctive features from the more common cutaneous form of malignant melanoma (cMM). At the molecular level, hMMs are characterized by large chromosomal aberrations rather than single-nucleotide mutations, typically observed in cMM. Given the scarcity of available cases, there have been many attempts to establish a reliable animal model. In pet dogs, Canine Oral Melanoma (COM) is the most common malignant tumor of the oral cavity, sharing clinical and histological aspects with hMM. To improve the knowledge about COM's genomic DNA alterations, in the present work, formalin-fixed, paraffin-embedded (FFPE) samples of COM from different European archives were collected to set up an array Comparative Genomic Hybridization (aCGH) analysis to estimate recurrent Copy Number Aberrations (CNAs). DNA was extracted in parallel from tumor and healthy fractions and 19 specimens were successfully submitted to labeling and competitive hybridization. Data were statistically analyzed through GISTIC2.0 and a pathway-enrichment analysis was performed with ClueGO. Recurrent gained regions were detected, affecting chromosomes CFA 10, 13 and 30, while lost regions involved chromosomes CFA 10, 11, 22, and 30. In particular, CFA 13 showed a whole-chromosome gain in 37% of the samples, while CFA 22 showed a whole-chromosome loss in 25%. A distinctive sigmoidal trend was observed in CFA 10 and 30 in 25 and 30% of the samples, respectively. Comparative analysis revealed that COM and hMM share common chromosomal changes in 32 regions. MAPK- and PI3K-related genes were the most frequently involved, while pathway analysis revealed statistically significant perturbation of cancer-related biological processes such as immune response, drug metabolism, melanocytes homeostasis, and neo-angiogenesis. The latter is a new evidence of a significant involvement of neovascularization-related pathways in COMs and can provide the rationale for future application in anti-cancer targeted therapies.
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Affiliation(s)
- Ginevra Brocca
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Italy
| | - Clarissa Zamboni
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Italy
| | | | - Silvia Ferro
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Italy
| | - Michael H Goldschmidt
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Massimo Castagnaro
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Italy
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9
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Bargelloni L, Babbucci M, Ferraresso S, Papetti C, Vitulo N, Carraro R, Pauletto M, Santovito G, Lucassen M, Mark FC, Zane L, Patarnello T. Draft genome assembly and transcriptome data of the icefish Chionodraco myersi reveal the key role of mitochondria for a life without hemoglobin at subzero temperatures. Commun Biol 2019; 2:443. [PMID: 31815198 PMCID: PMC6884616 DOI: 10.1038/s42003-019-0685-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 11/08/2019] [Indexed: 11/10/2022] Open
Abstract
Antarctic fish belonging to Notothenioidei represent an extraordinary example of radiation in the cold. In addition to the absence of hemoglobin, icefish show a number of other striking peculiarities including large-diameter blood vessels, high vascular densities, mitochondria-rich muscle cells, and unusual mitochondrial architecture. In order to investigate the bases of icefish adaptation to the extreme Southern Ocean conditions we sequenced the complete genome of the icefish Chionodraco myersi. Comparative analyses of the icefish genome with those of other teleost species, including two additional white-blooded and five red-blooded notothenioids, provided a new perspective on the evolutionary loss of globin genes. Muscle transcriptome comparative analyses against red-blooded notothenioids as well as temperate fish revealed the peculiar regulation of genes involved in mitochondrial function in icefish. Gene duplication and promoter sequence divergence were identified as genome-wide patterns that likely contributed to the broad transcriptional program underlying the unique features of icefish mitochondria.
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Affiliation(s)
- Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy
- Department of Land, Environment, Agriculture, and Forestry, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196 Rome, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy
| | - Chiara Papetti
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196 Rome, Italy
- Department of Biology, University of Padova, Via G. Colombo 3, 35131 Padua, Italy
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Roberta Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy
| | - Gianfranco Santovito
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196 Rome, Italy
| | - Magnus Lucassen
- Section of Integrative Ecophysiology, Alfred Wegener Institute Helmholtz. Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570 Germany
| | - Felix Christopher Mark
- Section of Integrative Ecophysiology, Alfred Wegener Institute Helmholtz. Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570 Germany
| | - Lorenzo Zane
- Department of Land, Environment, Agriculture, and Forestry, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196 Rome, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196 Rome, Italy
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10
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Zamboni C, Brocca G, Ferraresso S, Ferro S, Sammarco A, Dal Corso C, Iussich S, de Andres PJ, Martìnez de Merlo EM, Cavicchioli L, Zappulli V, Castagnaro M. Cyclin D1 immunohistochemical expression and somatic mutations in canine oral melanoma. Vet Comp Oncol 2019; 18:231-238. [PMID: 31503380 DOI: 10.1111/vco.12539] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 12/13/2022]
Abstract
Canine oral melanoma (COM) is the most frequent tumour with oral localization in dogs. Copy number gains and amplifications of CCND1, a gene coding for Cyclin D1, are the most frequent chromosomal aberrations described in human non-UV induced melanomas. Twenty-eight cases of COM were retrieved from paraffin-blocks archives. A total of 4 μm thick sections were immunostained with an antibody against human Cyclin D1 and Ki-67. Cyclin D1 and Ki-67 expressions were scored through two counting methods. DNA was extracted from 20 μm thick sections of formalin-fixed paraffin-embedded blocks. Pathological and surrounding healthy tissue was extracted independently. Cyclin D1 immunolabelling was detected in 69% (18/26) while Ki-67 was present in 88.5% (23/26) of cases. Statistical analysis revealed correlation between two counting methods for Cyclin D1 (r = 0.54; P = .004) and Ki-67 (r = 0.56; P = .003). The correlation found between Ki-67 and Cyclin D1 indexes in 16/26 cases labelled by both antibodies (r = 0.7947; P = .0002) suggests a possible use of Cyclin D1 index as prognostic marker. Polymerase chain reaction analysis on CCND1 coding sequence revealed the presence of nine somatic mutations in seven samples producing synonymous, missense and stop codons. Since none of the single-nucleotide polymorphisms was found to be recurrent, it is suggested that overexpression of Cyclin D1 may be the consequence of alterations of CCND1 upstream regions or other genetic aberrations not detectable with the methodology used in this study. Future studies are needed to verify the potential use of Cyclin D1 index as prognostic indicator and to highlight the molecular events responsible for Cyclin D1 overexpression in COMs.
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Affiliation(s)
- Clarissa Zamboni
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Ginevra Brocca
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Silvia Ferro
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Alessandro Sammarco
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Chiara Dal Corso
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Selina Iussich
- Department of Veterinary Sciences, University of Turin, Grugliasco, Turin, Italy
| | - Paloma J de Andres
- Department of Animal Medicine Surgery and Pathology, School of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Elena M Martìnez de Merlo
- Department of Animal Medicine Surgery and Pathology, School of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Laura Cavicchioli
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Valentina Zappulli
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Massimo Castagnaro
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
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11
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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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12
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Giannuzzi D, Marconato L, Cascione L, Comazzi S, Elgendy R, Pegolo S, Cecchinato A, Bertoni F, Aresu L, Ferraresso S. Mutational landscape of canine B-cell lymphoma profiled at single nucleotide resolution by RNA-seq. PLoS One 2019; 14:e0215154. [PMID: 31017932 PMCID: PMC6481796 DOI: 10.1371/journal.pone.0215154] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/27/2019] [Indexed: 12/30/2022] Open
Abstract
The genomic landscape in human B-cell lymphoma has revealed several somatic mutations and potentially relevant germline alterations affecting therapy and prognosis. Also, mutations originally described as somatic aberrations have been shown to confer cancer predisposition when occurring in the germline. The relevance of mutations in canine B-cell lymphoma is scarcely known and gene expression profiling has shown similar molecular signatures among different B-cell histotypes, suggesting other biological mechanisms underlining differences. Here, we present a highly accurate approach to identify single nucleotide variants (SNVs) in RNA-seq data obtained from 62 completely staged canine B-cell lymphomas and 11 normal B-cells used as controls. A customized variant discovery pipeline was applied and SNVs were found in tumors and differentiated for histotype. A number of known and not previously identified SNVs were significantly associated to MAPK signaling pathway, negative regulation of apoptotic process and cell death, B-cell activation, NF-kB and JAK-STAT signaling. Interestingly, no significant genetic fingerprints were found separating diffuse large B-cell lymphoma from indolent lymphomas suggesting that differences of genetic landscape are not the pivotal causative factor of indolent behavior. We also detected several variants in expressed regions of canine B-cell lymphoma and identified SNVs having a direct impact on genes. Using this brand-new approach the consequence of a gene variant is directly associated to expression. Further investigations are in progress to deeply elucidate the mechanisms by which altered genes pathways may drive lymphomagenesis and a higher number of cases is also demanded to confirm this evidence.
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Affiliation(s)
- Diana Giannuzzi
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
- * E-mail:
| | - Laura Marconato
- Centro Oncologico Veterinario, Sasso Marconi, Bologna, Italy
| | - Luciano Cascione
- Università della Svizzera italiana (USI), Institute of Oncology Research (IOR), Bellinzona, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Stefano Comazzi
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Ramy Elgendy
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sara Pegolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Legnaro, Padua, Italy
| | - Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Legnaro, Padua, Italy
| | - Francesco Bertoni
- Università della Svizzera italiana (USI), Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | - Luca Aresu
- Department of Veterinary Science, University of Turin, Grugliasco, Turin, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
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13
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Giannuzzi D, Marconato L, Elgendy R, Ferraresso S, Scarselli E, Fariselli P, Nicosia A, Pegolo S, Leoni G, Laganga P, Leone VF, Giantin M, Troise F, Dacasto M, Aresu L. Longitudinal transcriptomic and genetic landscape of radiotherapy response in canine melanoma. Vet Comp Oncol 2019; 17:308-316. [PMID: 30805995 DOI: 10.1111/vco.12473] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/20/2019] [Accepted: 02/25/2019] [Indexed: 12/22/2022]
Abstract
Canine malignant melanoma (MM) is a highly aggressive tumour with a low survival rate and represents an ideal spontaneous model for the human counterpart. Considerable progress has been recently obtained, but the therapeutic success for canine melanoma is still challenging. Little is known about the mechanisms beyond pathogenesis and melanoma development, and the molecular response to radiotherapy has never been explored before. A faster and deeper understanding of cancer mutational processes and developing mechanisms are now possible through next generation sequencing technologies. In this study, we matched whole exome and transcriptome sequencing in four dogs affected by MM at diagnosis and at disease progression to identify possible genetic mechanisms associated with therapy failure. According to previous studies, a genetic similarity between canine MM and its human counterpart was observed. Several somatic mutations were functionally related to MAPK, PI3K/AKT and p53 signalling pathways, but located in genes other than BRAF, RAS and KIT. At disease progression, several mutations were related to therapy effects. Natural killer cell-mediated cytotoxicity and several immune-system-related pathways resulted activated opening a new scenario on the microenvironment in this tumour. In conclusion, this study suggests a potential role of the immune system associated to radiotherapy in canine melanoma, but a larger sample size associated with functional studies are needed.
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Affiliation(s)
- Diana Giannuzzi
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Laura Marconato
- Centro Oncologico Veterinario, Sasso Marconi, Bologna, Italy
| | - Ramy Elgendy
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | | | - Piero Fariselli
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Alfredo Nicosia
- Nouscom AG, Basel, Switzerland.,Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c. a.r.l., Naples, Italy
| | - Sara Pegolo
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padua, Legnaro, Padua, Italy
| | | | - Paola Laganga
- Centro Oncologico Veterinario, Sasso Marconi, Bologna, Italy
| | - Vito F Leone
- Centro Oncologico Veterinario, Sasso Marconi, Bologna, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | | | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Luca Aresu
- Department of Veterinary Science, University of Turin, Grugliasco, Turin, Italy
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14
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Milan M, Maroso F, Dalla Rovere G, Carraro L, Ferraresso S, Patarnello T, Bargelloni L, Cardazzo B, Fariselli P. Tracing seafood at high spatial resolution using NGS-generated data and machine learning: Comparing microbiome versus SNPs. Food Chem 2019; 286:413-420. [PMID: 30827626 DOI: 10.1016/j.foodchem.2019.02.037] [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: 08/03/2018] [Revised: 01/16/2019] [Accepted: 02/11/2019] [Indexed: 11/25/2022]
Abstract
Developing reliable tools to trace food origin represents a major goal for producers and control authorities. Here, we test the hypothesis whether NGS-generated data could provide a reliable tool to ensure seafood traceability. As a test case, we used the Manila clam Ruditapes philippinarum, a bivalve mollusk of high commercial interest with worldwide distribution, collected in the Venice lagoon sites subjected to prohibition of clam harvesting because of chemical contamination as well as in authorized clam harvesting areas. The results obtained demonstrated that the geographic origin of Manila clam may be more accurately determined basing on microbiome data than single nucleotide polymorphisms. In particular, combining microbiome data with machine-learning techniques, we provide the experimental evidence that it is possible to trace the clam place of origin at high spatial resolution. Considering its low cost and portability, NGS-analysis of microbiome data might represent a cost-effective, high-resolution tool for reliable food traceability.
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Affiliation(s)
- Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy.
| | - Francesco Maroso
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Piero Fariselli
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
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15
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Aresu L, Ferraresso S, Marconato L, Cascione L, Napoli S, Gaudio E, Kwee I, Tarantelli C, Testa A, Maniaci C, Ciulli A, Hillmann P, Bohnacker T, Wymann MP, Comazzi S, Milan M, Riondato F, Rovere GD, Giantin M, Giannuzzi D, Bertoni F. New molecular and therapeutic insights into canine diffuse large B-cell lymphoma elucidates the role of the dog as a model for human disease. Haematologica 2018; 104:e256-e259. [PMID: 30545928 DOI: 10.3324/haematol.2018.207027] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Luca Aresu
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Italy
| | - Serena Ferraresso
- Dipartimento di Biomedicina Comparata e Alimentazione, Università degli Studi di Padova, Italy
| | | | - Luciano Cascione
- Università della Svizzera Italiana, Institute of Oncology Research, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sara Napoli
- Università della Svizzera Italiana, Institute of Oncology Research, Bellinzona, Switzerland
| | - Eugenio Gaudio
- Università della Svizzera Italiana, Institute of Oncology Research, Bellinzona, Switzerland
| | - Ivo Kwee
- Università della Svizzera Italiana, Institute of Oncology Research, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Dalle Molle Institute for Artificial Intelligence, Manno, Switzerland
| | - Chiara Tarantelli
- Università della Svizzera Italiana, Institute of Oncology Research, Bellinzona, Switzerland
| | - Andrea Testa
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Scotland, United Kingdom
| | - Chiara Maniaci
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Scotland, United Kingdom.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, England, United Kingdom
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Scotland, United Kingdom
| | | | | | | | - Stefano Comazzi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Italy
| | - Massimo Milan
- Dipartimento di Biomedicina Comparata e Alimentazione, Università degli Studi di Padova, Italy
| | - Fulvio Riondato
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Italy
| | - Giulia Dalla Rovere
- Dipartimento di Biomedicina Comparata e Alimentazione, Università degli Studi di Padova, Italy
| | - Mery Giantin
- Dipartimento di Biomedicina Comparata e Alimentazione, Università degli Studi di Padova, Italy
| | - Diana Giannuzzi
- Dipartimento di Biomedicina Comparata e Alimentazione, Università degli Studi di Padova, Italy
| | - Francesco Bertoni
- Università della Svizzera Italiana, Institute of Oncology Research, Bellinzona, Switzerland
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16
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Da Ros S, Aresu L, Ferraresso S, Zorzan E, Gaudio E, Bertoni F, Dacasto M, Giantin M. Validation of epigenetic mechanisms regulating gene expression in canine B-cell lymphoma: An in vitro and in vivo approach. PLoS One 2018; 13:e0208709. [PMID: 30533020 PMCID: PMC6289462 DOI: 10.1371/journal.pone.0208709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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] [Received: 04/18/2018] [Accepted: 11/21/2018] [Indexed: 01/26/2023] Open
MESH Headings
- Animals
- Cell Line, Tumor
- Dog Diseases/genetics
- Dog Diseases/metabolism
- Dogs
- Epigenesis, Genetic/drug effects
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/physiology
- Histone Deacetylase Inhibitors/pharmacology
- Lymph Nodes
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/veterinary
- Promoter Regions, Genetic
- RNA, Messenger/metabolism
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Affiliation(s)
- Silvia Da Ros
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Luca Aresu
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Eleonora Zorzan
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Eugenio Gaudio
- Università della Svizzera italiana, Institute of Oncology Research, Bellinzona, Switzerland
| | - Francesco Bertoni
- Università della Svizzera italiana, Institute of Oncology Research, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
- * E-mail:
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17
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Pauletto M, Manousaki T, Ferraresso S, Babbucci M, Tsakogiannis A, Louro B, Vitulo N, Quoc VH, Carraro R, Bertotto D, Franch R, Maroso F, Aslam ML, Sonesson AK, Simionati B, Malacrida G, Cestaro A, Caberlotto S, Sarropoulou E, Mylonas CC, Power DM, Patarnello T, Canario AVM, Tsigenopoulos C, Bargelloni L. Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish. Commun Biol 2018; 1:119. [PMID: 30271999 PMCID: PMC6123679 DOI: 10.1038/s42003-018-0122-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 01/12/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that sex-biased genes in S. aurata are similar in number and function, but evolved following strikingly divergent patterns compared with gonochoristic species, showing overall slower rates because of stronger functional constraints. Fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode of S. aurata, first maturing as male, then as female. To our knowledge, these findings represent the first genome-wide analysis on sex-biased loci in a hermaphrodite vertebrate species, demonstrating how having two sexes in the same individual profoundly affects the fate of a large set of evolutionarily relevant genes.
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Affiliation(s)
- Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Alexandros Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Bruno Louro
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Viet Ha Quoc
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Roberta Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Daniela Bertotto
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Rafaella Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Francesco Maroso
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | | | | | | | | | - Alessandro Cestaro
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Stefano Caberlotto
- Valle Cà Zuliani Società Agricola Srl, Via Timavo 76, 34074, Monfalcone, Gorizia, Italy
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Costantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Deborah M Power
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Adelino V M Canario
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Costas Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy.
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18
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Milan M, Dalla Rovere G, Smits M, Ferraresso S, Pastore P, Marin MG, Bogialli S, Patarnello T, Bargelloni L, Matozzo V. Ecotoxicological effects of the herbicide glyphosate in non-target aquatic species: Transcriptional responses in the mussel Mytilus galloprovincialis. Environ Pollut 2018; 237:442-451. [PMID: 29505984 DOI: 10.1016/j.envpol.2018.02.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 11/20/2017] [Revised: 01/26/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
Glyphosate has been the most widely used herbicide worldwide over the last three decades, raising increasing concerns for its potential impacts on environmental and human health. Recent studies revealed that glyphosate occurs in soil, surface water, and groundwater, and residues are found at all levels of the food chain, such as drinking water, plants, animals, and even in humans. While research has demonstrated that glyphosate can induce a broad range of biological effects in exposed organisms, the global molecular mechanisms of action still need to be elucidated, in particular for marine species. In this study, we characterized for the first time the molecular mechanisms of action of glyphosate in a marine bivalve species after exposure to environmentally realistic concentrations. To reach such a goal, Mediterranean mussels Mytilus galloprovincialis, an ecologically and economically relevant species, were exposed for 21 days to 10, 100, and 1000 μg/L and digestive gland transcriptional profiles were investigated through RNA-seq. Differential expression analysis identified a total of 111, 124, and 211 differentially regulated transcripts at glyphosate concentrations of 10, 100, and 1000 μg/L, respectively. Five genes were found consistently differentially expressed at all investigated concentrations, including SERP2, which plays a role in the protection of unfolded target proteins against degradation, the antiapoptotic protein GIMAP5, and MTMR14, which is involved in macroautophagy. Functional analysis of differentially expressed genes reveals the disruption of several key biological processes, such as energy metabolism and Ca2+ homeostasis, cell signalling, and endoplasmic reticulum stress response. Together, the results obtained suggest that the presence of glyphosate in the marine ecosystem should raise particular concern because of its significant effects even at the lowest concentration.
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Affiliation(s)
- M Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy.
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - M Smits
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy; Marine Environmental Science Laboratory (LEMAR), Université de Bretagne Occidentale -Rue Dumont d'Urville, 29280 Plouzané - IUEM Technopole Brest-Iroise, France
| | - S Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - P Pastore
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - M G Marin
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - S Bogialli
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - V Matozzo
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
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19
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Carraro R, Dalla Rovere G, Ferraresso S, Carraro L, Franch R, Toffan A, Pascoli F, Patarnello T, Bargelloni L. Development of a real-time PCR assay for rapid detection and quantification of Photobacterium damselae subsp. piscicida in fish tissues. J Fish Dis 2018; 41:247-254. [PMID: 28857188 DOI: 10.1111/jfd.12703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 06/07/2023]
Abstract
The availability of a rapid and accurate method for the diagnosis of Photobacterium damselae subsp. piscicida (Phdp), able to discriminate its strictly correlated subsp. damselae (Phdd), formally known as Vibrio damsela, is essential for managing fish pasteurellosis outbreaks in farmed fish. A single-step, high-sensitivity real-time PCR assay for simultaneous detection and quantification of P. damselae was designed targeting partial of the sequence of the bamB gene and tested for specificity and sensitivity on laboratory-generated samples as well as on experimentally infected seabream tissue samples. With a limit of detection (LOD) of one copy in pure bacterial DNA, the sensitivity was higher than all methods previously reported. Validation in target and non-target bacterial species proved the assay was able to discriminate Phdd-Phdp subspecies from diverse hosts/geographical origins and between non-target species. In addition, two SNPs in the target amplicon region determine two distinctive qPCR dissociation curves distinguishing between Phdp-Phdd. This is the first time that a molecular method for P. damselae diagnosis combines detection, quantification and subspecies identification in one step. The assay holds the potential to improve the knowledge of infection dynamics and the development of better strategies to control an important fish disease.
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Affiliation(s)
- R Carraro
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - S Ferraresso
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - L Carraro
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - R Franch
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - A Toffan
- Fish Virology Department, National Reference Laboratory for Fish, Crustacean and Mollusc Diseases, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - F Pascoli
- Fish Virology Department, National Reference Laboratory for Fish, Crustacean and Mollusc Diseases, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
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20
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Hampel M, Blasco J, Babbucci M, Ferraresso S, Bargelloni L, Milan M. Transcriptome analysis of the brain of the sea bream (Sparus aurata) after exposure to human pharmaceuticals at realistic environmental concentrations. Mar Environ Res 2017; 129:36-45. [PMID: 28434674 DOI: 10.1016/j.marenvres.2017.04.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 02/11/2017] [Revised: 04/09/2017] [Accepted: 04/09/2017] [Indexed: 06/07/2023]
Abstract
Human pharmaceuticals such as Acetaminophen, Atenolol and Carbamazepine are pseudo persistent aquatic pollutants with yet unknown sub-lethal effects at environmentally relevant concentrations. Gilthead seabream (Sparus aurata) were exposed to Acetaminophen: 31.90 ± 11.07 μg L-1; Atenolol: 0.95 ± 0.38 μg L-1 and Carbamazepine: 6.95 ± 0.13 μg L-1 in a 28 day flow through experiment to (1) determine whether exposure to low concentrations in the μg·L-1 range of the pharmaceuticals alters the brain transcriptome and, (2) identify different expression profiles and treatment specific modes of action and pathways. Despite low exposure concentrations, 411, 7 and 612 differently expressed transcripts were identified in the individual treatments with Acetaminophen, Atenolol and Carbamazepine, respectively. Functional analyses of differentially expressed genes revealed a significant over representation of several biological processes, cellular compartment features and molecular functions for both Acetaminophen and Carbamazepine treatments. Overall, the results obtained in seabream brain suggest similar physiological responses to those observed in humans also at environmental concentrations, as well as the existence of treatment specific processes that may be useful for the development of biomarkers of contamination.
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Affiliation(s)
- Miriam Hampel
- Department for Physical Chemistry, Faculty of Marine and Environmental Sciences, University of Cadiz, 11510 Puerto Real, Cadiz, Spain; University Institute for Marine Research (INMAR), 11510 Puerto Real, Cadiz, Spain.
| | - Julian Blasco
- Andalusian Institute for Marine Sciences, Department of Ecology and Coastal Management, Campus Universitario Río San Pedro s/n, 11519 Puerto Real, Spain
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, I-35020 Legnaro, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, I-35020 Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, I-35020 Legnaro, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, I-35020 Legnaro, Italy
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21
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Babbucci M, Ferraresso S, Pauletto M, Franch R, Papetti C, Patarnello T, Carnier P, Bargelloni L. An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax). Sci Rep 2016; 6:38673. [PMID: 27929136 PMCID: PMC5144136 DOI: 10.1038/srep38673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/11/2016] [Indexed: 12/13/2022] Open
Abstract
Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified. The two GWAS candidate markers were located on ChrX and Chr17, both in close proximity with the peaks of the two most significant QTLs. Notably, the SNP marker on Chr17 was positioned within the Sobp gene coding region, which plays a pivotal role in craniofacial development. The analysis of differentially expressed genes in jaw-deformed animals highlighted the “nervous system development” as a crucial pathway in MP. In particular, Zic2, a key gene for craniofacial morphogenesis in model species, was significantly down-regulated in MP-affected animals. Gene expression data revealed also a significant down-regulation of Sobp in deformed larvae. Our analyses, integrating transcriptomic and GWA methods, provide evidence for putative mechanisms underlying seabass jaw deformity.
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Affiliation(s)
- Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Rafaella Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Chiara Papetti
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Paolo Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
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22
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Cavicchioli L, Ferraresso S, Westmoreland S, Kaliyaperumal S, Knight H, Crossan C, Scobie L, Danesi A, Vadori M, Trez D, Badin RA, Hantraye P, Cozzi E. Posttransplant Lymphoproliferative Disorders in Neuronal Xenotransplanted Macaques. Vet Pathol 2016; 54:336-344. [PMID: 27694423 DOI: 10.1177/0300985816669407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Posttransplant lymphoproliferative disorders (PTLDs) are a heterogeneous group of lymphoid proliferations that occur in the setting of depressed T-cell function due to immunosuppressive therapy used following solid organ transplantation, hematopoietic stem cell transplantation, and also xenotransplantation. In the present study, 28 immunosuppressed parkinsonian Macaca fascicularis were intracerebrally injected with wild-type or CTLA4-Ig transgenic porcine xenografts to identify a suitable strategy to enable long-term cell survival, maturation, and differentiation. Nine of 28 (32%) immunosuppressed primates developed masses compatible with PTLD, located mainly in the gastrointestinal tract and/or nasal cavity. The masses were classified as monomorphic PTLD according to the World Health Organization classification. Immunohistochemistry and polymerase chain reaction (PCR) analyses revealed that the PTLDs were associated with macaca lymphocryptovirus as confirmed by double-labeling immunohistochemistry for CD20 and Epstein-Barr nuclear antigen 2 (EBNA-2), where the viral protein was located within the CD20+ neoplastic B cells. In sera from 3 distinct phases of the experimental life of the primates, testing by quantitative PCR revealed a progression of the viral load that paralleled the PTLD progression and no evidence of zoonotic transmission of porcine lymphotropic herpesvirus through xenoneuronal grafts. These data suggest that monitoring the variation of macaca lymphocryptovirus DNA in primates could be used as a possible early diagnostic tool for PTLD progression, allowing preemptive treatment such as immunosuppression therapy reduction.
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Affiliation(s)
- L Cavicchioli
- 1 Department of Comparative Biomedicine and Food Science, Padova University, Padova, Italy
| | - S Ferraresso
- 1 Department of Comparative Biomedicine and Food Science, Padova University, Padova, Italy
| | - S Westmoreland
- 2 New England Primate Research Center, Southborough, MA, USA
| | - S Kaliyaperumal
- 2 New England Primate Research Center, Southborough, MA, USA
| | - H Knight
- 2 New England Primate Research Center, Southborough, MA, USA
| | - C Crossan
- 3 Caledonian University, Glasgow, UK
| | - L Scobie
- 3 Caledonian University, Glasgow, UK
| | - A Danesi
- 1 Department of Comparative Biomedicine and Food Science, Padova University, Padova, Italy
| | | | - D Trez
- 1 Department of Comparative Biomedicine and Food Science, Padova University, Padova, Italy
| | - R Aron Badin
- 5 MIRCen, CEA UMR 9199, Fontenay-aux-Roses, France
| | - P Hantraye
- 5 MIRCen, CEA UMR 9199, Fontenay-aux-Roses, France
| | - E Cozzi
- 4 CORIT, Padova, Italy.,6 Padova General Hospital, Padova, Italy
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23
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Ferraresso S, Bonaldo A, Parma L, Buonocore F, Scapigliati G, Gatta PP, Bargelloni L. Ontogenetic onset of immune-relevant genes in the common sole (Solea solea). Fish Shellfish Immunol 2016; 57:278-292. [PMID: 27554393 DOI: 10.1016/j.fsi.2016.08.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 05/27/2016] [Revised: 07/25/2016] [Accepted: 08/19/2016] [Indexed: 06/06/2023]
Abstract
Fish are free-living organisms since initial stages of development and are exposed to numerous pathogens before their lymphoid organs have matured and adaptive immunity has developed. Susceptibility to diseases and juvenile mortality represent key critical factors for aquaculture. In this context, the characterization of the appearance kinetics of the immune system key members will be useful in understanding the ability of a particular species in generating immune protection against invading pathogens at different developmental stages. The present study characterized, for the first time, the transcriptional onset of un-explored relevant genes of both innate and adaptive immune system during the Solea solea ontogenesis. Gene expression profiles of immune relevant genes was investigated, by means of DNA microarray, in ten developmental stages, from hatching (1 day post-hatching, dph) to accomplishment of the juvenile form (33 dph). The obtained results revealed that transcripts encoding relevant members of innate immune repertoire, such as lysozyme, AMPs (hepcidin, β-defensin), PPRs and complement components are generally characterized by high expression levels at first stages (i.e. hatch and first feeding) indicating protection from environmental pathogens even at early development. Transcription of adaptive immune genes (i.e. Class I and class II MHC, TCRs) differs from that of the innate immune system. Their onset coincides with metamorphosis and larvae-to-juvenile transition, and likely overlaps with the appearance and maturation of the main lymphoid organs. Finally, data collected suggest that at the end of metamorphosis S. solea cell-mediated immune system hasn't still undergone full maturation.
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Affiliation(s)
- Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy.
| | - Alessio Bonaldo
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy.
| | - Luca Parma
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy.
| | - Francesco Buonocore
- Department for Innovation in Biological, Agro-food and Forest Systems, Tuscia University, Via San Camillo de Lellis s.n.c., 01100 Viterbo, Italy.
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-food and Forest Systems, Tuscia University, Via San Camillo de Lellis s.n.c., 01100 Viterbo, Italy.
| | - Pier Paolo Gatta
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy.
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy.
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24
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Cavicchioli L, Zanetti R, Ferraresso S, Crossan C, Barry PA, Boldrin M, Vadori M, Ferro S, Calabrese F, Scobie L, Cozzi E, Zappulli V. Expression of recipient cytomegalovirus in immunosuppressed and xenotransplanted Macaca fascicularis may be related to more severe gastrointestinal lesions. Xenotransplantation 2015; 22:135-43. [PMID: 25683577 DOI: 10.1111/xen.12153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 12/23/2014] [Indexed: 12/01/2022]
Abstract
BACKGROUND Xenotransplantation is a potential answer to the current organ shortage, but the risk of infections related to overimmunosuppression is an important parameter that may predict the recipient's long-term survival. Cytomegalovirus (CMV) in xenotransplanted and immunosuppressed primates is a well-known cause of disease particularly affecting the gastrointestinal (GI) tract and a zoonotic concern. METHODS Post-mortem sera and tissues from 45 immunosuppressed and xenografted Macaca fascicularis were evaluated for CMV using antisera specific for the immediate early 1 (IE1), anti-RhCMV, and QPCR for virus. RESULTS Serological analysis showed 100% positivity for the presence of CMV antibodies following the application of a specific test designed for RhCMV. Five of 45 primates showed typical lesions of CMV infection in the GI tract, including neutrophilic enteritis and inclusion bodies. Molecular analysis confirmed the presence of recipient's CMV in the tissues with CMV histopathology. Porcine CMV from the donor animals was not found in any of the CMV-specific IHC-positive recipients. CONCLUSION The presence of active CMV infection in animals intended for xenograft experiments can lead to severe gastrointestinal lesions that could impact the overall aims of the study. In such cases, the animals should be investigated using appropriate (non-human primate-specific) diagnostic tools prior to use and treated aggressively with state-of-the-art antiviral therapy.
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Affiliation(s)
- Laura Cavicchioli
- Department of Comparative Biomedicine and Food Science, Padua University, Padua, Italy
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25
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Mininni AN, Milan M, Ferraresso S, Petochi T, Di Marco P, Marino G, Livi S, Romualdi C, Bargelloni L, Patarnello T. Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature. BMC Genomics 2014; 15:765. [PMID: 25194679 PMCID: PMC4167152 DOI: 10.1186/1471-2164-15-765] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [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: 04/03/2014] [Accepted: 09/03/2014] [Indexed: 01/09/2023] Open
Abstract
Background Water temperature greatly influences the physiology and behaviour of teleost fish as other aquatic organisms. While fish are able to cope with seasonal temperature variations, thermal excursions outside their normal thermal range might exceed their ability to respond leading to severe diseases and death. Profound differences exist in thermal tolerance across fish species living in the same geographical areas, promoting for investigating the molecular mechanisms involved in susceptibility and resistance to low and high temperatures toward a better understanding of adaptation to environmental challenges. The gilthead sea bream, Sparus aurata, is particularly sensitive to cold and the prolonged exposure to low temperatures may lead to the "winter disease", a metabolic disorder that significantly affects the aquaculture productions along the Northern Mediterranean coasts during winter-spring season. While sea bream susceptibility to low temperatures has been extensively investigated, the cascade of molecular events under such stressful condition is not fully elucidated. Results In the present study two groups of wild sea bream were exposed for 21 days to two temperature regimes: 16 ± 0.3°C (control group) and 6.8 ± 0.3°C (cold-exposed group) and DNA microarray analysis of liver transcriptome was carried out at different time points during cold exposure. A large set of genes was found to be differentially expressed upon cold-exposure with increasingly relevant effects being observed after three weeks at low temperature. All major known responses to cold (i.e. anti-oxidant response, increased mitochondrial function, membrane compositional changes) were found to be conserved in the gilthead sea bream, while, evidence for a key role of unfolded protein response (UPR) to endoplasmic reticulum (ER) stress, during short- and long-term exposure to cold is reported here for the first time. Conclusions Transcriptome data suggest a scenario where oxidative stress, altered lipid metabolism, ATP depletion and protein denaturation converge to induce ER stress. The resulting UPR activation further promotes conditions for cell damage, and the inability to resolve ER stress leads to severe liver dysfunction and potentially to death. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-765) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy.
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Aricò A, Guadagnin E, Ferraresso S, Gelain ME, Iussich S, Rütgen BC, Mazzariol S, Marconato L, Aresu L. Platelet-derived growth factors and receptors in Canine Lymphoma. J Comp Pathol 2014; 151:322-8. [PMID: 25172054 DOI: 10.1016/j.jcpa.2014.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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: 05/06/2014] [Revised: 06/19/2014] [Accepted: 07/03/2014] [Indexed: 12/17/2022]
Abstract
Platelet-derived growth factors (PDGFs) belong to a family of polypeptide growth factors that signal through cell surface tyrosine kinase receptors to stimulate growth, proliferation and differentiation. Platelet-derived growth factor receptors (PDGFRs) are also considered important targets for specific kinase inhibitors in the treatment of several human tumours. The aim of this study was to investigate the role of PDGF-A, PDGF-B, PDGFR-α and PDGFR-β in canine lymphoma by determining gene and protein expression in lymph nodes of dogs with diffuse large B-cell lymphoma (DLBCL), peripheral T-cell lymphoma (PTCL), T-lymphoblastic lymphoma (T-LBL) and in healthy control dogs. One lymph node was also studied at the end of therapy in a subset of dogs in remission for DLBCL. In controls, PDGF-A, PDGFR-α and PDGFR-β mRNA levels were significantly higher than in DLBCLs, PTCLs and T-LBLs. However, PDGFR-α and PDGFR-β were minimally expressed by lymphocytes and plasma cells in normal lymph nodes as determined by immunohistochemistry, while neoplastic B and T cells showed the highest score (P <0.05). This discordant result may be compatible with the constitutive expression of these molecules by endothelial cells and fibroblasts in normal lymph nodes, thereby influencing gene expression results. Furthermore, these cells were not included in the immunohistochemical analysis. Similarly, dogs with DLBCL that were in remission at the end of therapy showed significantly higher gene expression of PDGFs and receptors than at the time of diagnosis and with an opposite trend to the protein assay. PDGF-B protein and mRNA were overexpressed in PTCLs and T-LBLs when compared with DLBCLs and controls (P <0.05). Additionally, there was a correlation between protein expression of PDGF-B and both PDGFRs in PTCLs and T-LBLs, suggesting an autocrine or paracrine loop in the aetiology of aggressive canine T-cell lymphomas. These data provide a rationale for the use of PDGFR antagonists in the therapy of aggressive T-cell lymphomas, but not in DLBCLs.
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Affiliation(s)
- A Aricò
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Agripolis, Legnaro, PD, Italy.
| | - E Guadagnin
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Agripolis, Legnaro, PD, Italy
| | - S Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Agripolis, Legnaro, PD, Italy
| | - M E Gelain
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Agripolis, Legnaro, PD, Italy
| | - S Iussich
- Department of Veterinary Science, University of Torino, Via Leonardo da Vinci 44, 10095 Grugliasco, TO, Italy
| | - B C Rütgen
- Clinical Pathology, Department of Pathobiology, University of Veterinary Medicine of Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - S Mazzariol
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Agripolis, Legnaro, PD, Italy
| | - L Marconato
- Centro Oncologico Veterinario, via San Lorenzo 1-4, 40037 Sasso Marconi, BO, Italy
| | - L Aresu
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Agripolis, Legnaro, PD, Italy
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Mazurais D, Ferraresso S, Gatta PP, Desbruyères E, Severe A, Corporeau C, Claireaux G, Bargelloni L, Zambonino-Infante JL. Identification of hypoxia-regulated genes in the liver of common sole (Solea solea) fed different dietary lipid contents. Mar Biotechnol (NY) 2014; 16:277-288. [PMID: 24091821 DOI: 10.1007/s10126-013-9545-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 09/15/2013] [Indexed: 06/02/2023]
Abstract
Coastal systems could be affected by hypoxic events brought about by global change. These areas are essential nursery habitats for several fish species including the common sole (Solea solea L.). Tolerance of fish to hypoxia depends on species and also on their physiological condition and nutritional status. Indeed, high dietary lipid content has been recently shown to negatively impact the resistance of sole to a severe hypoxic challenge. In order to study the molecular mechanisms involved in the early response to hypoxic stress, the present work examined the hepatic transcriptome in common sole fed diets with low and high lipid content, exposed to severe hypoxia. The activity of AMP-activated protein kinase (AMPK) was also investigated through the quantification of threonine-172 phosphorylation in the alpha subunit. The results show that hypoxia consistently regulates several actors involved in energy metabolism pathways and particularly AMPKα, as well as some involved in cell growth and maintenance or unfolded protein response. Our findings reveal that (1) the expression of genes involved in biological processes with high energy cost or implicated in aerobic ATP synthesis was down-regulated by hypoxia, contrary to genes involved in neoglucogenesis or in angiogenesis, (2) the consumption of high lipid induced regulation of metabolic pathways going against this energy saving, and (3) this control was fine-tuned by the regulation of several transcriptomic factors. These results provide insight into the biological processes involved in the hepatic response to hypoxic stress and underline the negative impact of high lipid consumption on the tolerance of common sole to hypoxia.
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Affiliation(s)
- David Mazurais
- Ifremer, UMR 6539 LEMAR, Unité de Physiologie Fonctionnelle des Organismes Marins, Ifremer, CS 10070, 29280, Plouzané, France,
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Aresu L, Aricò A, Ferraresso S, Martini V, Comazzi S, Riondato F, Giantin M, Dacasto M, Guadagnin E, Frayssinet P, Rouquet N, Drigo M, Marconato L. Minimal residual disease detection by flow cytometry and PARR in lymph node, peripheral blood and bone marrow, following treatment of dogs with diffuse large B-cell lymphoma. Vet J 2014; 200:318-24. [DOI: 10.1016/j.tvjl.2014.03.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 02/10/2014] [Accepted: 03/01/2014] [Indexed: 10/25/2022]
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Ferraresso S, Bresolin S, Aricò A, Comazzi S, Gelain ME, Riondato F, Bargelloni L, Marconato L, te Kronnie G, Aresu L. Epigenetic silencing of TFPI-2 in canine diffuse large B-cell lymphoma. PLoS One 2014; 9:e92707. [PMID: 24695110 PMCID: PMC3973630 DOI: 10.1371/journal.pone.0092707] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/25/2014] [Indexed: 12/18/2022] Open
Abstract
Epigenetic modifications are important early events during carcinogenesis. In particular, hypermethylation of CpG islands in the promoter region of tumor suppressor genes is a well-known mechanism of gene silencing that contributes to cancer development and progression. Tissue factor pathway inhibitor 2 (TFPI-2) is a tumor suppressor involved in invasiveness inhibition. Although TFPI-2 transcriptional silencing, through promoter hypermethylation, has been widely reported in several human malignancies, it has never been explored in lymphoma. In the present study TFPI-2 methylation and gene expression have been investigated in canine Diffuse Large B-cell lymphomas (cDLBCL). The methylation level of 23 CpGs located within the TFPI-2 promoter was investigated by bisulfite-specific PCR and next generation amplicon deep sequencing (GS Junior 454, Roche) in 22 cDLBCLs and 9 controls. For the same specimens, TFPI-2 gene expression was assessed by means of Real-time RT-PCR. Sequence analysis clearly demonstrated that TFPI2 is frequently hypermethylated in cDLBCL. Hypermethylation of the TFPI-2 promoter was found in 77% of DLBCLs (17 out of 22) and in one normal lymph node. Globally, dogs with DLBCL showed a mean methylation level significantly increased compared to controls (p<0.01) and analysis of hypermethylation by site identified 19 loci out of 23 (82%) with mean methylation levels from 2- to 120-fold higher in cDLBCL. Gene expression analysis confirmed a significant down-regulation of TFPI-2 (p<0.05) in DLBCLs compared with normal lymph nodes, suggesting that TFPI-2 hypermethylation negatively regulates its transcription. In addition, a significant positive correlation (p<0.01) was found between TFPI-2 methylation levels and age providing the first indication of age-associated epigenetic modifications in canine DLBCL. To conclude, our findings demonstrated that epigenetic dysregulation of TFPI-2, leading to its reduced expression, is frequently detected in canine DLBCL. In the next future, the aberrant TFPI-2 promoter hypermethylation may be considered in association with prognosis and therapy.
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Affiliation(s)
- Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Silvia Bresolin
- Department of Women’s and Children’s Health, University of Padova, Padova, Italy
| | - Arianna Aricò
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Stefano Comazzi
- Department of Animal Pathology Hygiene and Veterinary Public Health, University of Milano, Milano, Italy
| | - Maria Elena Gelain
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Fulvio Riondato
- Department Veterinary Science, University of Torino, Torino, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | | | - Geertruy te Kronnie
- Department of Women’s and Children’s Health, University of Padova, Padova, Italy
| | - Luca Aresu
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
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Bocchini N, Giantin M, Crivellente F, Ferraresso S, Faustinelli I, Dacasto M, Cristofori P. Molecular biomarkers of phospholipidosis in rat blood and heart after amiodarone treatment. J Appl Toxicol 2014; 35:90-103. [DOI: 10.1002/jat.2992] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Nicola Bocchini
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; viale dell'Università 16 I-35020 Legnaro (Padova) Italy
- Scuola di Dottorato in Scienze Veterinarie, indirizzo di Sanità pubblica e Patologia comparata; viale dell'Università 16 I-35020 Legnaro (Padova) Italy
| | - Mery Giantin
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; viale dell'Università 16 I-35020 Legnaro (Padova) Italy
| | | | - Serena Ferraresso
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; viale dell'Università 16 I-35020 Legnaro (Padova) Italy
| | - Ivo Faustinelli
- Preclinical Technologies; Aptuit, via Fleming 4 37135 Verona Italy
| | - Mauro Dacasto
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; viale dell'Università 16 I-35020 Legnaro (Padova) Italy
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Padoan E, Ferraresso S, Pegolo S, Castagnaro M, Barnini C, Bargelloni L. Real time RT-PCR analysis of inflammatory mediator expression in recurrent airway obstruction-affected horses. Vet Immunol Immunopathol 2013; 156:190-9. [PMID: 24176614 DOI: 10.1016/j.vetimm.2013.09.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 09/20/2013] [Accepted: 09/29/2013] [Indexed: 12/31/2022]
Abstract
The goal of the present study was to investigate mRNA expression levels of several cytokines and inflammatory mediators in broncho-alveolar lavage (BAL) fluid and respiratory epithelium in recurrent airway obstruction (RAO)-affected horses. RAO, also called heaves, is a common, performance-limiting, equine respiratory disease with clinical signs and pathophysiological similarities to human asthma, and characterized by bronchospasm, neutrophilic infiltration and increased mucus in the airways. Six RAO-affected horses were examined twice within 15 days and seven clinically healthy horses were examined for comparison. Quantitative real-time RT-PCR was used to assess mRNA expression of the inflammatory mediators IL-1β, IL-6, IL-8, IL-13, IL-17, TNFα, INFγ, TGFβ1, NFκ-β and TRL4 in bronchial biopsies and in BAL fluid. Gene expression levels were then compared with clinical signs, endoscopic examination, complete blood cell count, cytology of BAL fluid, histological examination of bronchial tissue and bacteriological and mycological examinations. Expression of IL1β, IL8, TLR4, TNFα, TGFβ1 and NFkβ transcripts was significantly up-regulated in RAO-affected compared to healthy horses. A similar trend, albeit not significant, was showed for IL17 and INFγ. A highly significant correlation was observed among IL-1β, IL8, TGFβ1, NFkβ, TRL4, and INFγ expression patterns as well as between expression levels of these genes and clinical parameters. In the present study, the comparison between clinically healthy and RAO-affected horses gave new insights on the cytokine expression in equine health and disease status. The identification of cytokines implicated in the pathogenesis of RAO may contribute to the diagnosis and treatment of this disease.
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Affiliation(s)
- E Padoan
- Equine Patavium Hospital, via G.Trieste n 21, Limena, PD, Italy; Department of Comparative Biomedicine and Food Science (BCA), University of Padua, Viale dell'Universita' 16, 35020 Legnaro, PD, Italy.
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Ferraresso S, Bonaldo A, Parma L, Cinotti S, Massi P, Bargelloni L, Gatta PP. Exploring the larval transcriptome of the common sole (Solea solea L.). BMC Genomics 2013; 14:315. [PMID: 23663263 PMCID: PMC3659078 DOI: 10.1186/1471-2164-14-315] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [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: 10/18/2012] [Accepted: 05/01/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The common sole (Solea solea) is a promising candidate for European aquaculture; however, the limited knowledge of the physiological mechanisms underlying larval development in this species has hampered the establishment of successful flatfish aquaculture. Although the fact that genomic tools and resources are available for some flatfish species, common sole genomics remains a mostly unexplored field. Here, we report, for the first time, the sequencing and characterisation of the transcriptome of S. solea and its application for the study of molecular mechanisms underlying physiological and morphological changes during larval-to-juvenile transition. RESULTS The S. solea transcriptome was generated from whole larvae and adult tissues using the Roche 454 platform. The assembly process produced a set of 22,223 Isotigs with an average size of 726 nt, 29 contigs and a total of 203,692 singletons. Of the assembled sequences, 75.2% were annotated with at least one known transcript/protein; these transcripts were then used to develop a custom oligo-DNA microarray. A total of 14,674 oligonucleotide probes (60 nt), representing 12,836 transcripts, were in situ synthesised onto the array using Agilent non-contact ink-jet technology. The microarray platform was used to investigate the gene expression profiles of sole larvae from hatching to the juvenile form. Genes involved in the ontogenesis of the visual system are up-regulated during the early stages of larval development, while muscle development and anaerobic energy pathways increase in expression over time. The gene expression profiles of key transcripts of the thyroid hormones (TH) cascade and the temporal regulation of the GH/IGF1 (growth hormone/insulin-like growth factor I) system suggest a pivotal role of these pathways in fish growth and initiation of metamorphosis. Pre-metamorphic larvae display a distinctive transcriptomic landscape compared to previous and later stages. Our findings highlighted the up-regulation of gene pathways involved in the development of the gastrointestinal system as well as biological processes related to folic acid and retinol metabolism. Additional evidence led to the formation of the hypothesis that molecular mechanisms of cell motility and ECM adhesion may play a role in tissue rearrangement during common sole metamorphosis. CONCLUSIONS Next-generation sequencing provided a good representation of the sole transcriptome, and the combination of different approaches led to the annotation of a high number of transcripts. The construction of a microarray platform for the characterisation of the larval sole transcriptome permitted the definition of the main processes involved in organogenesis and larval growth.
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Affiliation(s)
- Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy.
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Milan M, Ferraresso S, Ciofi C, Chelazzi G, Carrer C, Ferrari G, Pavan L, Patarnello T, Bargelloni L. Exploring the effects of seasonality and chemical pollution on the hepatopancreas transcriptome of the Manila clam. Mol Ecol 2013; 22:2157-72. [DOI: 10.1111/mec.12257] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 12/21/2012] [Accepted: 01/12/2013] [Indexed: 01/28/2023]
Affiliation(s)
- Massimo Milan
- Department of Comparative Biomedicine and Food Science; University of Padova; Viale dell'Università 16 35020 Legnaro (PD) Italy
- Department of Evolutionary Biology; University of Florence; Via Romana 17 50125 Florence Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science; University of Padova; Viale dell'Università 16 35020 Legnaro (PD) Italy
| | - Claudio Ciofi
- Department of Evolutionary Biology; University of Florence; Via Romana 17 50125 Florence Italy
| | - Guido Chelazzi
- Department of Evolutionary Biology; University of Florence; Via Romana 17 50125 Florence Italy
| | - Claudio Carrer
- Thetis S.P.A; Laboratorio Centro Studi Microinquinanti Organici (C.S.M.O.). Magistrato alle Acque; Via Asconio Pediano 9 35127 Padova
| | - Giorgio Ferrari
- Ufficio Tecnico per l'Antinquinamento; Magistrato alle Acque di Venezia; San Polo 737 Riva del Vin 30125 Venezia
| | - Lino Pavan
- G3 Industriale; Via Milano 18 30020 Marcon (VE)
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science; University of Padova; Viale dell'Università 16 35020 Legnaro (PD) Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science; University of Padova; Viale dell'Università 16 35020 Legnaro (PD) Italy
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Varriale S, Ferraresso S, Giacomelli S, Coscia MR, Bargelloni L, Oreste U. Evolutionary analysis of Antarctic teleost Toll-like receptor 2. Fish Shellfish Immunol 2012; 33:1076-1085. [PMID: 22960217 DOI: 10.1016/j.fsi.2012.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 07/02/2012] [Accepted: 07/25/2012] [Indexed: 06/01/2023]
Abstract
In the present study we address the investigation of TLR2 evolutionary selection in two Antarctic teleosts, Trematomus bernacchii (Nototheniidae) and Chionodraco hamatus (Channichthyidae). The nucleotide sequence of TLR2 has been determined in both species, encoding 20 leucine-rich repeats (LRRs) in the extracellular region and a classical Toll/IL-1R (TIR) domain in the intracellular region. High expression level of T. bernacchii TLR2 was found in spleen and skin. Using different methods we identified six codons that underwent Darwinian selection while 20 were found to be negatively selected. Molecular models of C. hamatus and T. bernacchii TLR2 ectodomain as well as of the TIR domain were built by Homology Modeling. Molecular Dynamics simulations were performed in water for 15 ns. The sites under positive selection were residing on the convex side of the solenoid, four out of six were in a 35-residue-long region including the central/N-terminal domain boundary: two in the external loop of LRR11 and the other two in the LRR12 loop. This region has been demonstrated to be the functional site of ligand interaction in human TLR2 structure. Antarctic TLR2 models showed more flexibility than TLR2 from the temperate species Gasterosteus aculeatus. These results suggest that the selective pressure has shaped TLR2 molecule in such a way that increased its activity under the peculiar Antarctic environmental conditions.
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Pegolo S, Gallina G, Montesissa C, Capolongo F, Ferraresso S, Pellizzari C, Poppi L, Castagnaro M, Bargelloni L. Transcriptomic markers meet the real world: finding diagnostic signatures of corticosteroid treatment in commercial beef samples. BMC Vet Res 2012; 8:205. [PMID: 23110699 PMCID: PMC3541986 DOI: 10.1186/1746-6148-8-205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 08/03/2012] [Accepted: 10/16/2012] [Indexed: 11/17/2022] Open
Abstract
Background The use of growth-promoters in beef cattle, despite the EU ban, remains a frequent practice. The use of transcriptomic markers has already proposed to identify indirect evidence of anabolic hormone treatment. So far, such approach has been tested in experimentally treated animals. Here, for the first time commercial samples were analyzed. Results Quantitative determination of Dexamethasone (DEX) residues in the urine collected at the slaughterhouse was performed by Liquid Chromatography-Mass Spectrometry (LC-MS). DNA-microarray technology was used to obtain transcriptomic profiles of skeletal muscle in commercial samples and negative controls. LC-MS confirmed the presence of low level of DEX residues in the urine of the commercial samples suspect for histological classification. Principal Component Analysis (PCA) on microarray data identified two clusters of samples. One cluster included negative controls and a subset of commercial samples, while a second cluster included part of the specimens collected at the slaughterhouse together with positives for corticosteroid treatment based on thymus histology and LC-MS. Functional analysis of the differentially expressed genes (3961) between the two groups provided further evidence that animals clustering with positive samples might have been treated with corticosteroids. These suspect samples could be reliably classified with a specific classification tool (Prediction Analysis of Microarray) using just two genes. Conclusions Despite broad variation observed in gene expression profiles, the present study showed that DNA-microarrays can be used to find transcriptomic signatures of putative anabolic treatments and that gene expression markers could represent a useful screening tool.
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Affiliation(s)
- Sara Pegolo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, Padova, Italy
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Geay F, Ferraresso S, Zambonino-Infante JL, Bargelloni L, Quentel C, Vandeputte M, Kaushik S, Cahu CL, Mazurais D. Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet. BMC Genomics 2011; 12:522. [PMID: 22017880 PMCID: PMC3377934 DOI: 10.1186/1471-2164-12-522] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 10/23/2011] [Indexed: 11/11/2022] Open
Abstract
Background Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have been shown to impact growth performance and immune system of fish as well as their subsequent nutritional value, particularly in marine fish species, which exhibit low capacity for biosynthesis of long-chain poly-unsaturated fatty acids (LC-PUFA). The main objective of the present study was to analyse the effects of a plant-based diet on the hepatic transcriptome of European sea bass (Dicentrarchus labrax). Results We report the first results obtained using a transcriptomic approach on the liver of two half-sibfamilies of the European sea bass that exhibit similar growth rates when fed a fish-based diet (FD), but significantly different growth rates when fed an all-plant diet (VD). Overall gene expression was analysed using oligo DNA microarrays (GPL9663). Statistical analysis identified 582 unique annotated genes differentially expressed between groups of fish fed the two diets, 199 genes regulated by genetic factors, and 72 genes that exhibited diet-family interactions. The expression of several genes involved in the LC-PUFA and cholesterol biosynthetic pathways was found to be up-regulated in fish fed VD, suggesting a stimulation of the lipogenic pathways. No significant diet-family interaction for the regulation of LC-PUFA biosynthesis pathways could be detected by microarray analysis. This result was in agreement with LC-PUFA profiles, which were found to be similar in the flesh of the two half-sibfamilies. In addition, the combination of our transcriptomic data with an analysis of plasmatic immune parameters revealed a stimulation of complement activity associated with an immunodeficiency in the fish fed VD, and different inflammatory status between the two half-sibfamilies. Biological processes related to protein catabolism, amino acid transaminations, RNA splicing and blood coagulation were also found to be regulated by diet, while the expression of genes involved in protein and ATP synthesis differed between the half-sibfamilies. Conclusions Overall, the combined gene expression, compositional and biochemical studies demonstrated a large panel of metabolic and physiological effects induced by total substitution of both FM and FO in the diets of European sea bass and revealed physiological characteristics associated with the two half-sibfamilies.
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Affiliation(s)
- Florian Geay
- Ifremer, UMR 1067, Departement Physiologie Fonctionnelle des Organismes Marins, Technopôle Brest-Iroise, BP 70, 29280 Plouzané, France
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Vieira FA, Gregório SF, Ferraresso S, Thorne MAS, Costa R, Milan M, Bargelloni L, Clark MS, Canario AVM, Power DM. Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus. BMC Genomics 2011; 12:490. [PMID: 21981800 PMCID: PMC3199283 DOI: 10.1186/1471-2164-12-490] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [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: 12/24/2010] [Accepted: 10/07/2011] [Indexed: 02/01/2023] Open
Abstract
Background Fish scales are an important reservoir of calcium and phosphorus and together with the skin function as an integrated barrier against environmental changes and external aggressors. Histological studies have revealed that the skin and scales regenerate rapidly in fish when they are lost or damaged. In the present manuscript the histological and molecular changes underlying skin and scale regeneration in fed and fasted sea bream (Sparus auratus) were studied using a microarray 3 and 7 days after scale removal to provide a comprehensive molecular understanding of the early stages of these processes. Results Histological analysis of skin/scales revealed 3 days after scale removal re-epithelisation and formation of the scale pocket had occurred and 53 and 109 genes showed significant up or down-regulation, respectively. Genes significantly up-regulated were involved in cell cycle regulation, cell proliferation and adhesion, immune response and antioxidant activities. 7 days after scale removal a thin regenerated scale was visible and only minor changes in gene expression occurred. In animals that were fasted to deplete mineral availability the expression profiles centred on maintaining energy homeostasis. The utilisation of fasting as a treatment emphasised the competing whole animal physiological requirements with regard to barrier repair, infection control and energy homeostasis. Conclusions The identification of numerous genes involved in the mitotic checkpoint and cell proliferation indicate that the experimental procedure may be useful for understanding cell proliferation and control in vertebrates within the context of the whole animal physiology. In response to skin damage genes of immune surveillance were up-regulated along with others involved in tissue regeneration required to rapidly re-establish barrier function. Additionally, candidate fish genes were identified that may be involved in cytoskeletal re-modelling, mineralization and stem cells, which are of potential use in aquaculture and fish husbandry, as they may impact on the ability of the fish to produce structural proteins, such as muscle, efficiently.
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Affiliation(s)
- Florbela A Vieira
- Comparative and Molecular Endocrinology Group, Centre for Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
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Tiago DM, Laizé V, Bargelloni L, Ferraresso S, Romualdi C, Cancela ML. Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate. BMC Genomics 2011; 12:310. [PMID: 21668972 PMCID: PMC3141667 DOI: 10.1186/1471-2164-12-310] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 06/13/2011] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Fish has been deemed suitable to study the complex mechanisms of vertebrate skeletogenesis and gilthead seabream (Sparus aurata), a marine teleost with acellular bone, has been successfully used in recent years to study the function and regulation of bone and cartilage related genes during development and in adult animals. Tools recently developed for gilthead seabream, e.g. mineralogenic cell lines and a 4 × 44K Agilent oligo-array, were used to identify molecular determinants of in vitro mineralization and genes involved in anti-mineralogenic action of vanadate. RESULTS Global analysis of gene expression identified 4,223 and 4,147 genes differentially expressed (fold change - FC > 1.5) during in vitro mineralization of VSa13 (pre-chondrocyte) and VSa16 (pre-osteoblast) cells, respectively. Comparative analysis indicated that nearly 45% of these genes are common to both cell lines and gene ontology (GO) classification is also similar for both cell types. Up-regulated genes (FC > 10) were mainly associated with transport, matrix/membrane, metabolism and signaling, while down-regulated genes were mainly associated with metabolism, calcium binding, transport and signaling. Analysis of gene expression in proliferative and mineralizing cells exposed to vanadate revealed 1,779 and 1,136 differentially expressed genes, respectively. Of these genes, 67 exhibited reverse patterns of expression upon vanadate treatment during proliferation or mineralization. CONCLUSIONS Comparative analysis of expression data from fish and data available in the literature for mammalian cell systems (bone-derived cells undergoing differentiation) indicate that the same type of genes, and in some cases the same orthologs, are involved in mechanisms of in vitro mineralization, suggesting their conservation throughout vertebrate evolution and across cell types. Array technology also allowed identification of genes differentially expressed upon exposure of fish cell lines to vanadate and likely involved in its anti-mineralogenic activity. Many were found to be unknown or they were never associated to bone homeostasis previously, thus providing a set of potential candidates whose study will likely bring insights into the complex mechanisms of tissue mineralization and bone formation.
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Affiliation(s)
- Daniel M Tiago
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
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Ferraresso S, Milan M, Pellizzari C, Vitulo N, Reinhardt R, Canario AVM, Patarnello T, Bargelloni L. Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity. BMC Genomics 2010; 11:354. [PMID: 20525278 PMCID: PMC2889902 DOI: 10.1186/1471-2164-11-354] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [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: 03/08/2010] [Accepted: 06/03/2010] [Indexed: 11/10/2022] Open
Abstract
Background The European sea bass (Dicentrarchus labrax) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying productive traits in farmed fish, and a step towards the application of marker assisted selection methods in this species. To this end, we report here on the development of an oligo DNA microarray for D. labrax. Results A database consisting of 19,048 unique transcripts was constructed, of which 12,008 (63%) could be annotated by similarity and 4,692 received a GO functional annotation. Two non-overlapping 60mer probes were designed for each unique transcript and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Probe design was positively completed for 19,035 target clusters; the oligo microarray was then applied to profile gene expression in mandibles and whole-heads of fish affected by prognathism, a skeletal malformation that strongly affects sea bass production. Statistical analysis identified 242 transcripts that are significantly down-regulated in deformed individuals compared to normal fish, with a significant enrichment in genes related to nervous system development and functioning. A set of genes spanning a wide dynamic range in gene expression level were selected for quantitative RT-PCR validation. Fold change correlation between microarray and qPCR data was always significant. Conclusions The microarray platform developed for the European sea bass has a high level of flexibility, reliability, and reproducibility. Despite the well known limitations in achieving a proper functional annotation in non-model species, sufficient information was obtained to identify biological processes that are significantly enriched among differentially expressed genes. New insights were obtained on putative mechanisms involved on mandibular prognathism, suggesting that bone/nervous system development might play a role in this phenomenon.
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Affiliation(s)
- Serena Ferraresso
- Department of Public Health, Comparative Pathology, and Veterinary Hygiene, Faculty of Veterinary Medicine, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
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Ferraresso S, Kuhl H, Milan M, Ritchie DW, Secombes CJ, Reinhardt R, Bargelloni L. Identification and characterisation of a novel immune-type receptor (NITR) gene cluster in the European sea bass, Dicentrarchus labrax, reveals recurrent gene expansion and diversification by positive selection. Immunogenetics 2009; 61:773-88. [PMID: 19851764 PMCID: PMC2921055 DOI: 10.1007/s00251-009-0398-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [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: 07/20/2009] [Accepted: 09/18/2009] [Indexed: 01/17/2023]
Abstract
In the last decade, a new gene family encoding non-rearranging receptors, called novel immune-type receptors (NITRs), has been discovered in teleost fish. NITRs belong to the immunoglobulin superfamily and represent an extraordinarily divergent and rapidly evolving gene complex. Genomic analysis of a region spanning 270 kb led to the discovery of a NITR gene cluster in the European sea bass (Dicentrarchus labrax). In total, 27 NITR genes and three putative pseudogenes, organised in a tandemly arrayed cluster, were identified. Sea bass NITR genes maintain the three major genomic organisations that appear to be essentially conserved among fish species along with new features presumably involving processes of intron loss, exon deletion and acquisition of new exons. Comparative and evolutionary analyses suggest that these receptors have evolved following a “birth-and-death” model of gene evolution in which duplication events together with lineage-specific gain and loss of individual members contributed to the rapid diversification of individual gene families. In this study, we demonstrate that species-specific gene expansions provide the raw material for diversifying, positive Darwinian selection favouring the evolution of a highly diverse array of molecules.
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Affiliation(s)
- Serena Ferraresso
- Department of Public Health, Comparative Pathology and Veterinary Hygiene, Faculty of Veterinary Medicine, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy.
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Carraro L, Ferraresso S, Cardazzo B, Romualdi C, Montesissa C, Gottardo F, Patarnello T, Castagnaro M, Bargelloni L. Expression profiling of skeletal muscle in young bulls treated with steroidal growth promoters. Physiol Genomics 2009; 38:138-48. [PMID: 19383624 DOI: 10.1152/physiolgenomics.00014.2009] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Dexamethasone (Dex), alone or in association with estrogens, is often illegally administered per os at very low dosage as a growth promoter in beef cattle, with effects that are opposite to the muscle wasting and atrophy induced by repeated administration at therapeutic dosages. In vitro and in vivo studies have investigated the catabolic effects of Dex at therapeutic doses on skeletal muscle, demonstrating an increase in the expression of GDF8 (myostatin) gene, a well-known negative regulator of skeletal muscle mass, in a dose-dependent way. This suggested a direct role of myostatin in Dex-induced muscle wasting. In the present study, an oligonucleotide microarray platform was used to compare expression profiles of beef cattle muscle in animals treated with either Dex or Dex plus 17-beta estradiol (Estr) administered at subtherapeutic dosage, against untreated controls. Data analysis demonstrates that the expression profiles were strongly affected by Dex treatment with hundreds of genes upregulated with relevant fold-change, whereas seven genes were downregulated including the myostatin gene. On the contrary, the number of differentially regulated genes was lower in response to the addition of Estr to the Dex treatment. Differentially regulated genes were analyzed to describe the effects of these treatments on muscle physiology, highlighting the importance of specific pathways (e.g., Wnt or cytokine signaling) and cellular processes (e.g., cell shape and motility). Finally, the observed differences in the expression profile will allow the development of indirect bio-markers to detect illegal Dex treatments in beef cattle using quantitative RT-PCR.
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Affiliation(s)
- L Carraro
- Department of Public Health, Comparative Pathology, and Veterinary Hygiene, University of Padova, Legnaro (PD), Italy
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Ferraresso S, Vitulo N, Mininni AN, Romualdi C, Cardazzo B, Negrisolo E, Reinhardt R, Canario AVM, Patarnello T, Bargelloni L. Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata). BMC Genomics 2008; 9:580. [PMID: 19055773 PMCID: PMC2648989 DOI: 10.1186/1471-2164-9-580] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [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: 07/17/2008] [Accepted: 12/03/2008] [Indexed: 01/15/2023] Open
Abstract
Background Aquaculture represents the most sustainable alternative of seafood supply to substitute for the declining marine fisheries, but severe production bottlenecks remain to be solved. The application of genomic technologies offers much promise to rapidly increase our knowledge on biological processes in farmed species and overcome such bottlenecks. Here we present an integrated platform for mRNA expression profiling in the gilthead sea bream (Sparus aurata), a marine teleost of great importance for aquaculture. Results A public data base was constructed, consisting of 19,734 unique clusters (3,563 contigs and 16,171 singletons). Functional annotation was obtained for 8,021 clusters. Over 4,000 sequences were also associated with a GO entry. Two 60mer probes were designed for each gene and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Platform reproducibility and accuracy were assessed on two early stages of sea bream development (one-day and four days old larvae). Correlation between technical replicates was always > 0.99, with strong positive correlation between paired probes. A two class SAM test identified 1,050 differentially expressed genes between the two developmental stages. Functional analysis suggested that down-regulated transcripts (407) in older larvae are mostly essential/housekeeping genes, whereas tissue-specific genes are up-regulated in parallel with the formation of key organs (eye, digestive system). Cross-validation of microarray data was carried out using quantitative qRT-PCR on 11 target genes, selected to reflect the whole range of fold-change and both up-regulated and down-regulated genes. A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates. Good concordance between qRT-PCR and microarray data was observed between 2- and 7-fold change, while fold-change compression in the microarray was present for differences greater than 10-fold in the qRT-PCR. Conclusion A highly reliable oligo-microarray platform was developed and validated for the gilthead sea bream despite the presently limited knowledge of the species transcriptome. Because of the flexible design this array will be able to accommodate additional probes as soon as novel unique transcripts are available.
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Affiliation(s)
- Serena Ferraresso
- Department of Public Health, Comparative Pathology and Veterinary Hygiene, Faculty of Veterinary Medicine, University of Padova, Viale dell'Università 16, Legnaro, Italy.
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