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Pallotti S, Picciolini M, Deiana G, Pediconi D, Antonini M, Napolioni V, Renieri C. Whole genome sequencing analysis of alpaca suggests TRPV3 as a candidate gene for the suri phenotype. BMC Genomics 2024; 25:185. [PMID: 38365607 PMCID: PMC10873959 DOI: 10.1186/s12864-024-10086-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Alpaca is a domestic South American camelid probably arising from the domestication of two wild camelids, the vicugna and the guanaco. Two phenotypes are described for alpaca, known as huacaya and suri. Huacaya fleece is characterized by compact, soft, and highly crimped fibers, while suri fleece is longer, straight, less crimped, and lustrous. The gene variants determining these phenotypes are still unknown, although previous studies suggested a dominant inheritance of the suri. Based on that, the aim of this study was the identification of the gene variants determining alpaca coat phenotypes through whole genome sequencing (WGS) analysis. RESULTS The sample used includes two test-cross alpaca families, suri × huacaya, which produced two offspring, one with the suri phenotype and one with the huacaya phenotype. The analyzed sample was expanded through the addition of WGS data from six vicugnas and six guanacos; this because we assumed the absence of the gene variants linked to the suri phenotype in these wild species. The analysis of gene variant segregation with the suri phenotype, coupled with the filtering of gene variants present in the wild species, disclosed the presence in all the suri samples of a premature termination codon (PTC) in TRPV3 (transient receptor potential cation channel subfamily V member 3), a gene known to be involved in hair growth and cycling, thermal sensation, cold tolerance and adaptation in several species. Mutations in TRPV3 were previously associated with the alteration of hair structure leading to an impaired formation of the hair canal and the hair shaft in mouse. This PTC in TRPV3, due to a G > T substitution (p.Glu475*), results in a loss of 290 amino acids from the canonical translated protein, plausibly leading to a physiological dysfunction. CONCLUSION The present results suggest that the suri phenotype may arise from a TRPV3 gene variant which may explain some of the suri features such as its longer hair fibre with lower number of cuticular scales compared to huacaya.
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Affiliation(s)
- Stefano Pallotti
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano s/n, 62032, Camerino, Italy.
| | | | - Giovanni Deiana
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
| | - Dario Pediconi
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
| | - Marco Antonini
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Roma, Italy
| | - Valerio Napolioni
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano s/n, 62032, Camerino, Italy
| | - Carlo Renieri
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
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Pallotti S, Picciolini M, Antonini M, Renieri C, Napolioni V. Genome-wide scan for runs of homozygosity in South American Camelids. BMC Genomics 2023; 24:470. [PMID: 37605116 PMCID: PMC10440933 DOI: 10.1186/s12864-023-09547-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. RESULTS A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. CONCLUSIONS The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.
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Affiliation(s)
- Stefano Pallotti
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy.
| | | | - Marco Antonini
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Roma, Italy
| | - Carlo Renieri
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
| | - Valerio Napolioni
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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Salvesi C, Silvi S, Fiorini D, Scortichini S, Sagratini G, Palermo FA, De Leone R, Egidi N, Fatone L, Cifani C, Amedei A, Scocchera F, Morici M, Gatto B, Mannucci F, Valeriani V, Malavasi M, Servili S, Casula A, Cresci A, Corradetti I, Carpi F, Picciolini M, Coman MM, Verdenelli MC. Impact of a probiotic diet on wellbeing of healthy senior:
THE PROBIOSENIOR PROJECT. J Appl Microbiol 2022; 133:2941-2953. [DOI: 10.1111/jam.15747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Chiara Salvesi
- Scuola di Bioscienze e Medicina Veterinaria University of Camerino Camerino Italy
| | - Stefania Silvi
- Scuola di Bioscienze e Medicina Veterinaria University of Camerino Camerino Italy
| | - Dennis Fiorini
- Scuola di Scienze e Tecnologie University of Camerino Camerino Italy
| | | | - Gianni Sagratini
- Scuola del Farmaco e dei Prodotti della Salute University of Camerino Camerino Italy
| | - Francesco A. Palermo
- Scuola di Bioscienze e Medicina Veterinaria University of Camerino Camerino Italy
| | - Renato De Leone
- Scuola di Scienze e Tecnologie University of Camerino Camerino Italy
| | - Nadaniela Egidi
- Scuola di Scienze e Tecnologie University of Camerino Camerino Italy
| | - Lorella Fatone
- Scuola di Scienze e Tecnologie University of Camerino Camerino Italy
| | - Carlo Cifani
- Scuola del Farmaco e dei Prodotti della Salute University of Camerino Camerino Italy
| | - Amedeo Amedei
- Dipartimento di Medicina Sperimentale e Clinica, Università di Firenze Firenze Italy
| | | | - Mara Morici
- COOSS Marche Cooperativa Sociale Onlus Ancona Italy
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Napolioni V, Bianconi F, Potenza R, Carpi FM, Ludovini V, Picciolini M, Tofanetti FR, Bufalari A, Pallotti S, Poggi C, Anile M, Daddi N, Venuta F, Puma F, Vannucci J. Genome-wide expression of the residual lung reacting to experimental Pneumonectomy. BMC Genomics 2021; 22:881. [PMID: 34872491 PMCID: PMC8650537 DOI: 10.1186/s12864-021-08171-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Background Acute or chronic irreversible respiratory failure may occur in patients undergoing pneumonectomy. Aim of this study was to determine transcriptome expression changes after experimental pneumonectomy in swine model. Experimental left pneumonectomy was performed in five pigs under general anaesthesia. Both the resected and the remaining lung, after 60 post-operative completely uneventful days, underwent genome-wide bulk RNA-Sequencing (RNA-Seq). Results Histological analysis showed dilation of air spaces and rupture of interalveolar septa. In addition, mild inflammation, no fibrosis, radial stretch of the bronchus, strong enlargement of airspaces and thinning of the blood supply were observed. Bioinformatic analyses of bulk RNA-Seq data identified 553 Differentially Expressed Genes (DEGs) at adjusted P-value below 0.001, between pre- and post-pneumonectomy. The top 10 up-regulated DEGs were Edn1, Areg, Havcr2, Gadd45g, Depp1, Cldn4, Atf3, Myc, Gadd45b, Socs3; the top 10 down-regulated DEGs were Obscn, Cdkn2b, ENSSSCG00000015738, Prrt2, Amer1, Flrt3, Efnb2, Tox3, Znf793, Znf365. Leveraging digital cytometry tools, no difference in cellular abundance was found between the two experimental groups, while the analysis of cell type-specific gene expression patterns highlighted a striking predominance of macrophage-specific genes among the DEGs. DAVID-based gene ontology analysis showed a significant enrichment of “Extrinsic apoptotic signaling pathway” (FDR q = 7.60 × 10− 3) and “Response to insulin” (FDR q = 7.60 × 10− 3) genes, along with an enrichment of genes involved as “Negative regulators of DDX58/IFIH1 signaling” (FDR q = 7.50 × 10− 4) found by querying the REACTOME pathway database. Gene network analyses indicated a general dysregulation of gene inter-connections. Conclusion This translational genomics study highlighted the existence both of individual genes, mostly dysregulated in certain cellular populations (e.g., macrophages), and gene-networks involved in pulmonary reaction after left pneumonectomy. Their involvement in lung homeostasis is largely supported by previous studies, carried out both in humans and in other animal models (under homeostatic or disease-related conditions), that adopted candidate-gene approaches. Overall, the present findings represent a preliminary assessment for future, more focused, studies on compensatory lung adaptation, pulmonary regeneration and functional reload. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08171-3.
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Affiliation(s)
- Valerio Napolioni
- Genomic and Molecular Epidemiology (GAME) Lab., School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | | | - Rossella Potenza
- Department of Thoracic Surgery, University of Perugia Medical School, Perugia, Italy.,Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | | | - Vienna Ludovini
- Department of Medical Oncology, S. Maria Della Misericordia Hospital, Perugia, Italy
| | | | - Francesca R Tofanetti
- Department of Medical Oncology, S. Maria Della Misericordia Hospital, Perugia, Italy
| | - Antonello Bufalari
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Stefano Pallotti
- Genetics and Animal Breeding Group, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Camilla Poggi
- Department of Thoracic Surgery, University of Rome Sapienza, Policlinico Umberto I, Viale del Policlinico 155, 00161, Rome, Italy
| | - Marco Anile
- Department of Thoracic Surgery, University of Rome Sapienza, Policlinico Umberto I, Viale del Policlinico 155, 00161, Rome, Italy
| | - Niccolò Daddi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Federico Venuta
- Department of Thoracic Surgery, University of Rome Sapienza, Policlinico Umberto I, Viale del Policlinico 155, 00161, Rome, Italy
| | - Francesco Puma
- Department of Thoracic Surgery, University of Perugia Medical School, Perugia, Italy
| | - Jacopo Vannucci
- Department of Thoracic Surgery, University of Rome Sapienza, Policlinico Umberto I, Viale del Policlinico 155, 00161, Rome, Italy.
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Carpi FM, Coman MM, Silvi S, Picciolini M, Verdenelli MC, Napolioni V. Comprehensive pan-genome analysis of Lactiplantibacillus plantarum complete genomes. J Appl Microbiol 2021; 132:592-604. [PMID: 34216519 PMCID: PMC9290807 DOI: 10.1111/jam.15199] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/18/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
Aims The aim of this work was to refine the taxonomy and the functional characterization of publicly available Lactiplantibacillus plantarum complete genomes through a pan‐genome analysis. Particular attention was paid in depicting the probiotic potential of each strain. Methods and results Complete genome sequence of 127 L. plantarum strains, without detected anomalies, was downloaded from NCBI. Roary analysis of L. plantarum pan‐genome identified 1436 core, 414 soft core, 1858 shell and 13,203 cloud genes, highlighting the ‘open’ nature of L. plantarum pan‐genome. Identification and characterization of plasmid content, mobile genetic elements, adaptative immune system and probiotic marker genes (PMGs) revealed unique features across all the L. plantarum strains included in the present study. Considering our updated list of PMGs, we determined that approximatively 70% of the PMGs belongs to the core/soft‐core genome. Conclusions The comparative genomic analysis conducted in this study provide new insights into the genomic content and variability of L. plantarum. Significance and Impact of the Study This study provides a comprehensive pan‐genome analysis of L. plantarum, including the largest number (N = 127) of complete L. plantarum genomes retrieved from publicly available repositories. Our effort aimed to determine a solid reference panel for the future characterization of newly sequenced L. plantarum strains useful as probiotic supplements.
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Affiliation(s)
| | | | - Stefania Silvi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | | | | | - Valerio Napolioni
- Genomic and Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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Consoli F, Barbieri G, Picciolini M, Medicina D, Bugatti M, Tovazzi V, Liserre B, Zambelli C, Zorzi F, Berruti A, Giurisato E, Vermi W. A Rare Complex BRAF Mutation Involving Codon V600 and K601 in Primary Cutaneous Melanoma: Case Report. Front Oncol 2020; 10:1056. [PMID: 32754440 PMCID: PMC7367153 DOI: 10.3389/fonc.2020.01056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/27/2020] [Indexed: 01/09/2023] Open
Abstract
BRAF is one of the most common mutated kinases detected in human cancer, particularly in cases of primary cutaneous melanomas (PCM). Mutations of the BRAF proto-oncogene, at the p.V600 codon, has been detected in more than 50% of primary and metastatic melanoma cells in clinical samples. In addition to the most frequent BRAF p.V600E mutation, corresponding to the single base pair substitution c.1799T>A, rarer mutations, within and outside the V600 codon, have been described. Expectedly, BRAF and MEK inhibitors (or their combination) have been poorly explored as potential therapeutic strategies in metastatic melanomas harboring this rare mutation. By using a set of sequencing techniques and immunohistochemistry, this work reports the genomic and clinical features of two melanoma patients showing a rare complex mutation affecting codon V600 and K601 of the BRAF gene, leading to a V600E2; K601I change. Specifically, these two patients show a distinct clinical behavior and significantly differ in their responses to BRAF and MEK inhibitors. Indeed, although this treatment has proven to be effective and safe in both cases, the observed variability between the two patients resulted as a direct consequence of the baseline extent of brain involvement, intracranial treatment failure as well as on the PTEN status.
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Affiliation(s)
| | | | | | - Daniela Medicina
- Unit of Anatomic Pathology, Spedali Civili di Brescia, Brescia, Italy
| | - Mattia Bugatti
- Unit of Anatomic Pathology, Spedali Civili di Brescia, Brescia, Italy
| | - Valeria Tovazzi
- Unit of Medical Oncology, Spedali Civili di Brescia, Brescia, Italy
| | - Barbara Liserre
- Department of Pathology, Fondazione Poliambulanza, Brescia, Italy
| | - Claudia Zambelli
- Unit of Anatomic Pathology, Spedali Civili di Brescia, Brescia, Italy
| | - Fausto Zorzi
- Department of Pathology, Fondazione Poliambulanza, Brescia, Italy
| | - Alfredo Berruti
- Unit of Medical Oncology, Spedali Civili di Brescia, Brescia, Italy.,Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy
| | - Emanuele Giurisato
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Department of Biotechnology Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - William Vermi
- Unit of Medical Oncology, Spedali Civili di Brescia, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
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7
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Ambrosio MR, Mundo L, Gazaneo S, Picciolini M, Vara PS, Sayed S, Ginori A, Lo Bello G, Del Porro L, Navari M, Ascani S, Yonis A, Leoncini L, Piccaluga PP, Lazzi S. MicroRNAs sequencing unveils distinct molecular subgroups of plasmablastic lymphoma. Oncotarget 2017; 8:107356-107373. [PMID: 29296171 PMCID: PMC5746073 DOI: 10.18632/oncotarget.22219] [Citation(s) in RCA: 21] [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: 06/20/2017] [Accepted: 09/08/2017] [Indexed: 11/25/2022] Open
Abstract
Plasmablastic lymphoma (PBL) is an aggressive lymphoma, often arising in the context of immunodeficiency and associated with Epstein-Barr virus (EBV) infection. The most frequently detected genetic alteration is the deregulation of MYC gene through the translocation - t(8;14)(q24;q32). The diagnosis of PBL is often challenging because it has an overlap in morphology, immunophenotype, cytogenetics and virus association with other lymphomas and plasma cell neoplasms; further, its molecular basis remains elusive. In the present study we aimed to better define the possible contribution of EBV infection as well as miRNA deregulation in PBL pathogenesis. We studied 23 cases of PBL, 19 Burkitt lymphomas (BL), and 17 extra-medullary plasmacytoma (EMPC). We used qPCR and immunohistochemistry to assess EBV latency patterns, while micro-RNA (miRNA) profiling was performed by next generation sequencing (Illumina) and validated by qPCR. Our analysis revealed a non-canonical EBV latency program with the partial expression of some proteins characterizing latency II and the activation of an abortive lytic cycle. Moreover, we identified miRNA signatures discriminating PBL from BL and EMPC. Interestingly, based on the miRNA profile, PBL appeared constituted by two discrete subgroups more similar to either BL or EMPC, respectively. This pattern was confirmed in an independent set of cases studied by qPCR and corresponded to different clinico-pathological features in the two groups, including HIV infection, MYC rearrangement and disease localization. In conclusion, we uncovered for the first time 1) an atypical EBV latency program in PBL; 2) a miRNA signature distinguishing PBL from the closest malignant counterparts; 3) the molecular basis of PBL heterogeneity.
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Affiliation(s)
| | - Lucia Mundo
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Siena, Italy
| | - Sara Gazaneo
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Siena, Italy
| | | | | | | | - Alessandro Ginori
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Siena, Italy
- Pathology Unit, Ospedale Civico di Carrara, Carrara, Italy
| | - Giuseppe Lo Bello
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Siena, Italy
| | - Leonardo Del Porro
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Siena, Italy
| | - Mohsen Navari
- Research Center of Advanced Technologies in Medicine, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
- Department of Experimental, Diagnostic, and Experimental Medicine, Bologna University School of Medicine, Bologna, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Stefano Ascani
- Section of Pathology, Azienda Ospedaliera S. Maria di Terni, University of Perugia, Perugia, Italy
| | | | - Lorenzo Leoncini
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Siena, Italy
| | - Pier Paolo Piccaluga
- Department of Experimental, Diagnostic, and Experimental Medicine, Bologna University School of Medicine, Bologna, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Stefano Lazzi
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Siena, Italy
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Mundo L, Ambrosio MR, Picciolini M, Lo Bello G, Gazaneo S, Del Porro L, Lazzi S, Navari M, Onyango N, Granai M, Bellan C, De Falco G, Gibellini D, Piccaluga PP, Leoncini L. Unveiling Another Missing Piece in EBV-Driven Lymphomagenesis: EBV-Encoded MicroRNAs Expression in EBER-Negative Burkitt Lymphoma Cases. Front Microbiol 2017; 8:229. [PMID: 28298901 PMCID: PMC5331039 DOI: 10.3389/fmicb.2017.00229] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/01/2017] [Indexed: 12/20/2022] Open
Abstract
Epstein–Barr virus (EBV) is a gammaherpesvirus linked to a number of lymphoid and epithelial malignancies, including Burkitt lymphoma (BL) in which its frequency ranges from 30% in sporadic cases to 100% in the endemic ones. The possible contribution of EBV to BL pathogenesis is largely unknown. It has been suggested that EBV may be associated with all of the cases, including those diagnosed as EBV negative by a mechanism of hit-and-run. Early during oncogenesis, viral genes are essential for initiating disease. Progressively, viral genome is lost to escape the immune system and host mutations accumulate in proto-oncogenic cell. The main problem with the hit-and-run hypothesis is the lack of evidence in primary tumors. The routine methods applied to detect the virus [i.e., immunohistochemistry and EBV-encoded RNAs (EBER) in situ hybridization (ISH)] have a low specificity and accuracy. The aim of this study was to identify the most suitable method to detect EBV infection in pathology samples by applying conventional and non-conventional methods (i.e., EBV-microRNAs detection and EBV viral load measurement). We investigated a total of 10 cases and we found that all the samples (n = 6) diagnosed as EBV negative by immunohistochemistry and EBER-ISH demonstrated the presence of EBV-microRNAs and EBV genome. This points at the possibility that EBV might have contributed to lymphomagenesis in all our patients, and propose microRNAs detection as the most specific and sensitive tool to recognize EBV vestiges. It is worth noting that our data would have considerable implications for EBV-related diseases control. By using anti-EBV vaccines, one could potentially prevent also some cancers less suspected of a viral origin because of viral genome loss.
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Affiliation(s)
- Lucia Mundo
- Section of Pathology, Department of Medical Biotechnology, University of Siena Siena, Italy
| | - Maria R Ambrosio
- Section of Pathology, Department of Medical Biotechnology, University of Siena Siena, Italy
| | | | - Giuseppe Lo Bello
- Section of Pathology, Department of Medical Biotechnology, University of Siena Siena, Italy
| | - Sara Gazaneo
- Section of Pathology, Department of Medical Biotechnology, University of Siena Siena, Italy
| | - Leonardo Del Porro
- Section of Pathology, Department of Medical Biotechnology, University of Siena Siena, Italy
| | - Stefano Lazzi
- Section of Pathology, Department of Medical Biotechnology, University of Siena Siena, Italy
| | - Mohsen Navari
- Department of Experimental, Diagnostic, and Experimental Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine Bologna, Italy
| | - Noel Onyango
- Department of Clinical Medicine and Therapeutics, University of Nairobi Nairobi, Kenya
| | - Massimo Granai
- Section of Pathology, Department of Medical Biotechnology, University of Siena Siena, Italy
| | - Cristiana Bellan
- Section of Pathology, Department of Medical Biotechnology, University of Siena Siena, Italy
| | - Giulia De Falco
- School of Biological and Chemical Sciences, Queen Mary University of London London, UK
| | - Davide Gibellini
- Virology Unit, Department of Diagnostic and Public Health, University of Verona Verona, Italy
| | - Pier P Piccaluga
- Department of Experimental, Diagnostic, and Experimental Medicine, S. Orsola-Malpighi Hospital, Bologna University School of MedicineBologna, Italy; Euro-Mediterranean Institute of Science and TechnologyPalermo, Italy
| | - Lorenzo Leoncini
- Section of Pathology, Department of Medical Biotechnology, University of Siena Siena, Italy
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9
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Mancini MV, Spaccapelo R, Damiani C, Accoti A, Tallarita M, Petraglia E, Rossi P, Cappelli A, Capone A, Peruzzi G, Valzano M, Picciolini M, Diabaté A, Facchinelli L, Ricci I, Favia G. Paratransgenesis to control malaria vectors: a semi-field pilot study. Parasit Vectors 2016; 9:140. [PMID: 26965746 PMCID: PMC4787196 DOI: 10.1186/s13071-016-1427-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria still remains a serious health burden in developing countries, causing more than 1 million deaths annually. Given the lack of an effective vaccine against its major etiological agent, Plasmodium falciparum, and the growing resistance of this parasite to the currently available drugs repertoire and of Anopheles mosquitoes to insecticides, the development of innovative control measures is an imperative to reduce malaria transmission. Paratransgenesis, the modification of symbiotic organisms to deliver anti-pathogen effector molecules, represents a novel strategy against Plasmodium development in mosquito vectors, showing the potential to reduce parasite development. However, the field application of laboratory-based evidence of paratransgenesis imposes the use of more realistic confined semi-field environments. METHODS Large cages were used to evaluate the ability of bacteria of the genus Asaia expressing green fluorescent protein (Asaia (gfp)), to diffuse in Anopheles stephensi and Anopheles gambiae target mosquito populations. Asaia (gfp) was introduced in large cages through the release of paratransgenic males or by sugar feeding stations. Recombinant bacteria transmission was directly detected by fluorescent microscopy, and further assessed by molecular analysis. RESULTS Here we show the first known trial in semi-field condition on paratransgenic anophelines. Modified bacteria were able to spread at high rate in different populations of An. stephensi and An. gambiae, dominant malaria vectors, exploring horizontal ways and successfully colonising mosquito midguts. Moreover, in An. gambiae, vertical and trans-stadial diffusion mechanisms were demonstrated. CONCLUSIONS Our results demonstrate the considerable ability of modified Asaia to colonise different populations of malaria vectors, including pecies where its association is not primary, in large environments. The data support the potential to employ transgenic Asaia as a tool for malaria control, disclosing promising perspective for its field application with suitable effector molecules.
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Affiliation(s)
| | - Roberta Spaccapelo
- Department of Experimental Medicine, Centro di Genomica Funzionale, University of Perugia, Perugia, Italy
| | - Claudia Damiani
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, Camerino, Italy
| | - Anastasia Accoti
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, Camerino, Italy
| | - Mario Tallarita
- Department of Experimental Medicine, Centro di Genomica Funzionale, University of Perugia, Perugia, Italy
| | - Elisabetta Petraglia
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, Camerino, Italy
| | - Paolo Rossi
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, Camerino, Italy
| | - Alessia Cappelli
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, Camerino, Italy
| | - Aida Capone
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, Camerino, Italy
| | - Giulia Peruzzi
- Department of Experimental Medicine, Centro di Genomica Funzionale, University of Perugia, Perugia, Italy
| | - Matteo Valzano
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, Camerino, Italy
| | - Matteo Picciolini
- Department of Experimental Medicine, Centro di Genomica Funzionale, University of Perugia, Perugia, Italy
| | - Abdoulaye Diabaté
- Institut de Recherche en Sciences de la Sante (IRSS), Direction Regionale de l'Ouest (DRO), BP 390, Bobo Dioulasso, Burkina Faso
| | - Luca Facchinelli
- Department of Experimental Medicine, Centro di Genomica Funzionale, University of Perugia, Perugia, Italy
| | - Irene Ricci
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, Camerino, Italy
| | - Guido Favia
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino, Camerino, Italy.
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10
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Drumo R, Pesciaroli M, Ruggeri J, Tarantino M, Chirullo B, Pistoia C, Petrucci P, Martinelli N, Moscati L, Manuali E, Pavone S, Picciolini M, Ammendola S, Gabai G, Battistoni A, Pezzotti G, Alborali GL, Napolioni V, Pasquali P, Magistrali CF. Salmonella enterica Serovar Typhimurium Exploits Inflammation to Modify Swine Intestinal Microbiota. Front Cell Infect Microbiol 2016; 5:106. [PMID: 26835435 PMCID: PMC4722131 DOI: 10.3389/fcimb.2015.00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/28/2015] [Indexed: 12/28/2022] Open
Abstract
Salmonella enterica serovar Typhimurium is an important zoonotic gastrointestinal pathogen responsible for foodborne disease worldwide. It is a successful enteric pathogen because it has developed virulence strategies allowing it to survive in a highly inflamed intestinal environment exploiting inflammation to overcome colonization resistance provided by intestinal microbiota. In this study, we used piglets featuring an intact microbiota, which naturally develop gastroenteritis, as model for salmonellosis. We compared the effects on the intestinal microbiota induced by a wild type and an attenuated S. Typhimurium in order to evaluate whether the modifications are correlated with the virulence of the strain. This study showed that Salmonella alters microbiota in a virulence-dependent manner. We found that the wild type S. Typhimurium induced inflammation and a reduction of specific protecting microbiota species (SCFA-producing bacteria) normally involved in providing a barrier against pathogens. Both these effects could contribute to impair colonization resistance, increasing the host susceptibility to wild type S. Typhimurium colonization. In contrast, the attenuated S. Typhimurium, which is characterized by a reduced ability to colonize the intestine, and by a very mild inflammatory response, was unable to successfully sustain competition with the microbiota.
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Affiliation(s)
- Rosanna Drumo
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di SanitàRome, Italy; Department of Comparative Biomedicine and Food Science, University of PaduaPadua, Italy
| | - Michele Pesciaroli
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di SanitàRome, Italy; VISAVET Health Surveillance Centre, Universidad Complutense MadridMadrid, Spain
| | - Jessica Ruggeri
- Department of Veterinary Diagnostic, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna Brescia, Italy
| | - Michela Tarantino
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità Rome, Italy
| | - Barbara Chirullo
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità Rome, Italy
| | - Claudia Pistoia
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità Rome, Italy
| | - Paola Petrucci
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità Rome, Italy
| | - Nicola Martinelli
- Department of Veterinary Diagnostic, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna Brescia, Italy
| | - Livia Moscati
- Research and Development Area, Istituto Zooprofilattico Sperimentale dell'Umbria e della Marche Perugia, Italy
| | - Elisabetta Manuali
- Research and Development Area, Istituto Zooprofilattico Sperimentale dell'Umbria e della Marche Perugia, Italy
| | - Silvia Pavone
- Research and Development Area, Istituto Zooprofilattico Sperimentale dell'Umbria e della Marche Perugia, Italy
| | - Matteo Picciolini
- Department of Experimental Medicine, University of Perugia Perugia, Italy
| | - Serena Ammendola
- Department of Biology, University of Roma Tor Vergata Rome, Italy
| | - Gianfranco Gabai
- Department of Comparative Biomedicine and Food Science, University of Padua Padua, Italy
| | | | - Giovanni Pezzotti
- Research and Development Area, Istituto Zooprofilattico Sperimentale dell'Umbria e della Marche Perugia, Italy
| | - Giovanni L Alborali
- Department of Veterinary Diagnostic, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna Brescia, Italy
| | - Valerio Napolioni
- Department of Experimental Medicine, University of Perugia Perugia, Italy
| | - Paolo Pasquali
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità Rome, Italy
| | - Chiara F Magistrali
- Research and Development Area, Istituto Zooprofilattico Sperimentale dell'Umbria e della Marche Perugia, Italy
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11
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Dritsou V, Topalis P, Windbichler N, Simoni A, Hall A, Lawson D, Hinsley M, Hughes D, Napolioni V, Crucianelli F, Deligianni E, Gasperi G, Gomulski LM, Savini G, Manni M, Scolari F, Malacrida AR, Arcà B, Ribeiro JM, Lombardo F, Saccone G, Salvemini M, Moretti R, Aprea G, Calvitti M, Picciolini M, Papathanos PA, Spaccapelo R, Favia G, Crisanti A, Louis C. A draft genome sequence of an invasive mosquito: an Italian Aedes albopictus. Pathog Glob Health 2015; 109:207-20. [PMID: 26369436 PMCID: PMC4727573 DOI: 10.1179/2047773215y.0000000031] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The draft genome sequence of Italian specimens of the Asian tiger mosquito Aedes (Stegomyia) albopictus (Diptera: Culicidae) was determined using a standard NGS (next generation sequencing) approach. The size of the assembled genome is comparable to that of Aedes aegypti; the two mosquitoes are also similar as far as the high content of repetitive DNA is concerned, most of which is made up of transposable elements. Although, based on BUSCO (Benchmarking Universal Single-Copy Orthologues) analysis, the genome assembly reported here contains more than 99% of protein-coding genes, several of those are expected to be represented in the assembly in a fragmented state. We also present here the annotation of several families of genes (tRNA genes, miRNA genes, the sialome, genes involved in chromatin condensation, sex determination genes, odorant binding proteins and odorant receptors). These analyses confirm that the assembly can be used for the study of the biology of this invasive vector of disease.
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Affiliation(s)
- Vicky Dritsou
- Polo d'Innovazione di Genomica, Genetica e Biologia (Polo GGB), Loc. S. Andrea delle Fratte, Perugia, Italy
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Nikolai Windbichler
- Imperial College London Department of Life Sciences, South Kensington Campus, UK
| | - Alekos Simoni
- Imperial College London Department of Life Sciences, South Kensington Campus, UK
| | - Ann Hall
- Imperial College London Department of Life Sciences, South Kensington Campus, UK
| | - Daniel Lawson
- European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genomes Campus, Cambridge, Cambridgeshire, UK
| | - Malcolm Hinsley
- European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genomes Campus, Cambridge, Cambridgeshire, UK
| | - Daniel Hughes
- European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genomes Campus, Cambridge, Cambridgeshire, UK
| | - Valerio Napolioni
- Polo d'Innovazione di Genomica, Genetica e Biologia (Polo GGB), Loc. S. Andrea delle Fratte, Perugia, Italy
| | - Francesca Crucianelli
- Polo d'Innovazione di Genomica, Genetica e Biologia (Polo GGB), Loc. S. Andrea delle Fratte, Perugia, Italy
| | - Elena Deligianni
- Institute of Molecular Biology and Biotechnology Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Giuliano Gasperi
- Department of Biology and Biotechnology University of Pavia, Italy
| | | | - Grazia Savini
- Department of Biology and Biotechnology University of Pavia, Italy
| | - Mosè Manni
- Department of Biology and Biotechnology University of Pavia, Italy
| | | | | | - Bruno Arcà
- Department of Public Health and Infectious Diseases – Division of Parasitology Sapienza University of Rome, Italy
| | - José M. Ribeiro
- National Institute of Allergy and Infectious Diseases Bethesda, MD, USA
| | - Fabrizio Lombardo
- Department of Public Health and Infectious Diseases – Division of Parasitology Sapienza University of Rome, Italy
| | | | - Marco Salvemini
- Department of Biology University of Naples Federico II, Italy
| | - Riccardo Moretti
- ENEA – Italian National Agency for New Technologies Energy and Sustainable Economic Development, CR Casaccia, Rome, Italy
| | - Giuseppe Aprea
- ENEA – Italian National Agency for New Technologies Energy and Sustainable Economic Development, CR Casaccia, Rome, Italy
| | - Maurizio Calvitti
- ENEA – Italian National Agency for New Technologies Energy and Sustainable Economic Development, CR Casaccia, Rome, Italy
| | - Matteo Picciolini
- Polo d'Innovazione di Genomica, Genetica e Biologia (Polo GGB), Loc. S. Andrea delle Fratte, Perugia, Italy
| | | | | | - Guido Favia
- Scuola di Bioscienze e Medicina Veterinaria, University of Camerino, Italy
| | | | - Christos Louis
- Correspondence to: Christos Louis, IMBB-FORTH, N. Plastira 100, Vassilika Vouton, GR-700 13 Heraklion, Crete, Greece.
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12
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Romani L, Zelante T, Palmieri M, Napolioni V, Picciolini M, Velardi A, Aversa F, Puccetti P. The cross-talk between opportunistic fungi and the mammalian host via microbiota's metabolism. Semin Immunopathol 2014; 37:163-71. [PMID: 25404119 DOI: 10.1007/s00281-014-0464-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/04/2014] [Indexed: 12/26/2022]
Abstract
An increased understanding of the importance of microbiota in shaping the host's immune and metabolic activities has rendered fungal interactions with their hosts more complex than previously appreciated. It is now clear that a three-way interaction between host, fungi, and microbiota dictates the types of host-fungus relationship. Indeed, microbial dysbiosis predisposes to a variety of chronic fungal infections and diseases at local and distant sites. By correlating changes in metabolite profiles with microbiota metagenomic composition, we have defined a functional node whereby certain bacteria species contribute to host-fungal symbiosis and mucosal homeostasis. A tryptophan catabolic pathway is exploited by commensal lactobacilli and the mammalian host to increase fitness in response to Candida albicans by inducing resistance and tolerance mechanisms of antifungal immunity. Much like lactobacilli in the gut, Firmicutes change significantly in the airways during aspergillosis. The aryl hydrocarbon receptor has a pivotal role in connecting tryptophan catabolism by microbial communities and the host's own pathway of tryptophan degradation through the enzyme indoleamine 2,3-dioxygenase 1. These data suggest that the study of the human microbiota in the trans-omics era, with a focus on metagenomics and metabonomics, is providing novel insights into the regulation of host immune responsiveness to fungi.
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Affiliation(s)
- Luigina Romani
- Department of Experimental Medicine, University of Perugia, Polo Unico Sant'Andrea delle Fratte, 06132, Perugia, Italy,
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13
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Concetti F, Carpi FM, Nabissi M, Picciolini M, Santoni G, Napolioni V. The functional polymorphism rs73598374:G>A (p.Asp8Asn) of the ADA gene is associated with telomerase activity and leukocyte telomere length. Eur J Hum Genet 2014; 23:267-70. [PMID: 24896148 DOI: 10.1038/ejhg.2014.102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 03/18/2014] [Accepted: 04/30/2014] [Indexed: 11/09/2022] Open
Abstract
Recent evidence demonstrated a relevant role of adenosine deaminase (ADA) in replicative senescence of T cells through its capacity to modulate telomerase activity (TA). Herein, we tested the impact of the functional polymorphism ADA rs73598374:G>A (c.22G>A, p.Asp8Asn) on telomere biology, by measuring TA and leukocyte telomere length (LTL) in healthy subjects selected according to rs73598374 genotype. rs73598374-A carriers showed lower TA (P=0.019) and shorter LTL (P=0.003), respectively, compared to G/G carriers. rs73598374-A carriers showed a stronger cross-sectional age reduction of LTL (r=-0.314, P=0.005) compared to G/G carriers (r=-0.243, P=0.022). The reduced ADA activity associated to rs73598374-A variant predisposes those carriers to display higher levels of adenosine compared to G/G carriers. Consequently, it may lead to an accelerated process of replicative senescence, causing a stronger reduction of TA and in turn shorter LTL. In conclusion, the crucial role played by replicative senescence of the immune system in several human diseases and in the aging process underscores the relevance of the present findings and also spurs interest into the possible involvement of rs73598374 in shaping the susceptibility to several age-related diseases.
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Affiliation(s)
| | - Francesco M Carpi
- School of Biosciences and Biotechnologies, University of Camerino, Camerino, Italy
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Nicolazzi EL, Picciolini M, Strozzi F, Schnabel RD, Lawley C, Pirani A, Brew F, Stella A. SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock. BMC Genomics 2014; 15:123. [PMID: 24517501 PMCID: PMC3923093 DOI: 10.1186/1471-2164-15-123] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [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: 09/03/2013] [Accepted: 02/06/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Currently, six commercial whole-genome SNP chips are available for cattle genotyping, produced by two different genotyping platforms. Technical issues need to be addressed to combine data that originates from the different platforms, or different versions of the same array generated by the manufacturer. For example: i) genome coordinates for SNPs may refer to different genome assemblies; ii) reference genome sequences are updated over time changing the positions, or even removing sequences which contain SNPs; iii) not all commercial SNP ID's are searchable within public databases; iv) SNPs can be coded using different formats and referencing different strands (e.g. A/B or A/C/T/G alleles, referencing forward/reverse, top/bottom or plus/minus strand); v) Due to new information being discovered, higher density chips do not necessarily include all the SNPs present in the lower density chips; and, vi) SNP IDs may not be consistent across chips and platforms. Most researchers and breed associations manage SNP data in real-time and thus require tools to standardise data in a user-friendly manner. DESCRIPTION Here we present SNPchiMp, a MySQL database linked to an open access web-based interface. Features of this interface include, but are not limited to, the following functions: 1) referencing the SNP mapping information to the latest genome assembly, 2) extraction of information contained in dbSNP for SNPs present in all commercially available bovine chips, and 3) identification of SNPs in common between two or more bovine chips (e.g. for SNP imputation from lower to higher density). In addition, SNPchiMp can retrieve this information on subsets of SNPs, accessing such data either via physical position on a supported assembly, or by a list of SNP IDs, rs or ss identifiers. CONCLUSIONS This tool combines many different sources of information, that otherwise are time consuming to obtain and difficult to integrate. The SNPchiMp not only provides the information in a user-friendly format, but also enables researchers to perform a large number of operations with a few clicks of the mouse. This significantly reduces the time needed to execute the large number of operations required to manage SNP data.
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