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Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample. Int J Mol Sci 2022; 23:ijms23126725. [PMID: 35743173 PMCID: PMC9223851 DOI: 10.3390/ijms23126725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.
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Messelodi D, Giuliani C, Cipriani F, Armuzzi S, di Palmo E, Garagnani P, Bertelli L, Astolfi A, Luiselli D, Ricci G, Pession A. C5 and SRGAP3 Polymorphisms Are Linked to Paediatric Allergic Asthma in the Italian Population. Genes (Basel) 2022; 13:214. [PMID: 35205259 PMCID: PMC8871526 DOI: 10.3390/genes13020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
Asthma is a complex and heterogeneous disease, caused by the interaction between genetic and environmental factors with a predominant allergic background in children. The role of specific genes in asthmatic bronchial reactivity is still not clear, probably because of the many common pathways shared with other allergic disorders. This study is focused on 11 SNPs possibly related to asthma that were previously identified in a GWAS study. The genetic variability of these SNPs has been analysed in a population of 773 Italian healthy controls, and the presence of an association between the polymorphisms and the asthma onset was evaluated performing genotyping analysis on 108 children affected with asthma compared with the controls. Moreover, a pool of 171 patients with only allergic rhinoconjunctivitis has been included in the case-control analysis. The comparison of allele frequencies in asthmatic patients versus healthy controls identified two SNPs-rs1162394 (p = 0.019) and rs25681 (p = 0.044)-associated with the asthmatic condition, which were not differentially distributed in the rhinoconjunctivitis group. The rs25681 SNP, together with three other SNPs, also resulted in not being homogenously distributed in the Italian population. The significantly higher frequency of the rs25681 and rs1162394 SNPs (located, respectively, in the C5 and SRGAP3 genes) in the asthmatic population suggests an involvement of these genes in the asthmatic context, playing a role in increasing the inflammatory condition that may influence asthma onset and clinical course.
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Affiliation(s)
- Daria Messelodi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy;
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology, Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
| | - Francesca Cipriani
- Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (F.C.); (E.d.P.); (L.B.); (A.P.)
| | - Silvia Armuzzi
- Institute of Hematology “Seràgnoli”, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138 Bologna, Italy; (P.G.); (A.A.)
| | - Emanuela di Palmo
- Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (F.C.); (E.d.P.); (L.B.); (A.P.)
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138 Bologna, Italy; (P.G.); (A.A.)
| | - Luca Bertelli
- Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (F.C.); (E.d.P.); (L.B.); (A.P.)
| | - Annalisa Astolfi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138 Bologna, Italy; (P.G.); (A.A.)
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Donata Luiselli
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage (DBC), Ravenna Campus, University of Bologna, 40126 Bologna, Italy;
| | - Giampaolo Ricci
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy;
| | - Andrea Pession
- Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (F.C.); (E.d.P.); (L.B.); (A.P.)
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Curcio A, Malovini A, Mazzanti A, Memmi M, Gambelli P, La Rosa F, Bloise R, Indolfi C, Bellazzi R, Napolitano C. Identification of a SCN5A founder mutation causing sudden death, Brugada syndrome, and conduction blocks in Southern Italy. Heart Rhythm 2021; 18:1698-1706. [PMID: 34245912 DOI: 10.1016/j.hrthm.2021.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND The genetic architecture of Brugada syndrome (BrS) is emerging as an increasingly complex area of investigation. The identification of genetically homogeneous populations can provide mechanistic insights and improve genotype-phenotype correlation. OBJECTIVE To characterize and define the clinical implications of a novel BrS founder mutation. Using a haplotype-based approach we investigated whether 2 SCN5A genetic variants could derive from founder events. METHODS Single nucleotide polymorphisms were genotyped in 201 subjects, haplotypes reconstructed, and mutational age estimated. Clinical phenotypes and historical records were collected. RESULTS A SCN5A variant (c.3352C>T; p.Gln1118Ter) was identified in 3 probands with BrS originating from south Italy. The same mutation was identified in a proband from central Italy and in 1 U.S. resident subject with Italian ancestry. The 5 individuals carried a common core haplotype, whose frequency was extremely low in local noncarrier probands and in population controls (0%-6.06%). The clinical presentation included multigenerational dominant transmission of Brugada electrocardiographic pattern, high incidence of sudden cardiac death (SCD), and cardiac conduction defects (CCD). We reconstructed 7-generation pedigrees with common geographic origin. Variant's age estimates suggested that origin of the p.Gln1118Ter dates back 76 generations (95% confidence interval: 28-200). A second SCN5A variant (c.5350G>A; p.Glu1784Lys) identified in the region did not show similar founder signal. CONCLUSION p.Gln1118Ter is a novel BrS/CCD/SCD founder mutation. We illustrate how these findings provide insights on the inheritance patterns and phenotypes associated with SCN5A mutation.
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Affiliation(s)
- Antonio Curcio
- Division of Cardiology, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Alberto Malovini
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri IRCCS, Pavia, Italy
| | - Andrea Mazzanti
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri IRCCS, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-Heart)
| | - Mirella Memmi
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri IRCCS, Pavia, Italy
| | - Patrick Gambelli
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri IRCCS, Pavia, Italy
| | - Francesca La Rosa
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri IRCCS, Pavia, Italy
| | - Raffaella Bloise
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri IRCCS, Pavia, Italy
| | - Ciro Indolfi
- Division of Cardiology, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy; Mediterranea Cardiocentro, Naples, Italy
| | - Riccardo Bellazzi
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri IRCCS, Pavia, Italy; Faculty of Engineering, University of Pavia, Pavia, Italy
| | - Carlo Napolitano
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri IRCCS, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-Heart).
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New DNA Methylation Signals for Malignant Pleural Mesothelioma Risk Assessment. Cancers (Basel) 2021; 13:cancers13112636. [PMID: 34071989 PMCID: PMC8199167 DOI: 10.3390/cancers13112636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Our study investigated DNA methylation differences in easily accessible white blood cells (WBCs) between malignant pleural mesothelioma (MPM) cases and asbestos-exposed cancer-free controls. A multiple regression model highlighted that the methylation level of two single CpGs (cg03546163 in FKBP5 and cg06633438 in MLLT1) are independent MPM markers. The epigenetic changes at the FKBP5 and MLLT1 genes were robustly associated with MPM in asbestos-exposed subjects. Interaction analyses showed that MPM cases and cancer-free controls showed DNAm differences which may be linked to asbestos exposure. Abstract Malignant pleural mesothelioma (MPM) is a rare and aggressive neoplasm. Patients are usually diagnosed when current treatments have limited benefits, highlighting the need for noninvasive tests aimed at an MPM risk assessment tool that might improve life expectancy. Three hundred asbestos-exposed subjects (163 MPM cases and 137 cancer-free controls), from the same geographical region in Italy, were recruited. The evaluation of asbestos exposure was conducted considering the frequency, the duration and the intensity of occupational, environmental and domestic exposure. A genome-wide methylation array was performed to identify novel blood DNA methylation (DNAm) markers of MPM. Multiple regression analyses adjusting for potential confounding factors and interaction between asbestos exposure and DNAm on the MPM odds ratio were applied. Epigenome-wide analysis (EWAS) revealed 12 single-CpGs associated with the disease. Two of these showed high statistical power (99%) and effect size (>0.05) after false discovery rate (FDR) multiple comparison corrections: (i) cg03546163 in FKBP5, significantly hypomethylated in cases (Mean Difference in beta values (MD) = −0.09, 95% CI = −0.12|−0.06, p = 1.2 × 10−7), and (ii) cg06633438 in MLLT1, statistically hypermethylated in cases (MD = 0.07, 95% CI = 0.04|0.10, p = 1.0 × 10−6). Based on the interaction analysis, asbestos exposure and epigenetic profile together may improve MPM risk assessment. Above-median asbestos exposure and hypomethylation of cg03546163 in FKBP5 (OR = 20.84, 95% CI = 8.71|53.96, p = 5.5 × 10−11) and hypermethylation of cg06633438 in MLLT1 (OR = 11.71, 95% CI = 4.97|29.64, p = 5.9 × 10−8) genes compared to below-median asbestos exposure and hyper/hypomethylation of single-CpG DNAm, respectively. Receiver Operation Characteristics (ROC) for Case-Control Discrimination showed a significant increase in MPM discrimination when DNAm information was added in the model (baseline model, BM: asbestos exposure, age, gender and white blood cells); area under the curve, AUC = 0.75; BM + cg03546163 at FKBP5. AUC = 0.89, 2.1 × 10−7; BM + cg06633438 at MLLT1. AUC = 0.89, 6.3 × 10−8. Validation and replication procedures, considering independent sample size and a different DNAm analysis technique, confirmed the observed associations. Our results suggest the potential application of DNAm profiles in blood to develop noninvasive tests for MPM risk assessment in asbestos-exposed subjects.
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First Bronze Age Human Mitogenomes from Calabria (Grotta Della Monaca, Southern Italy). Genes (Basel) 2021; 12:genes12050636. [PMID: 33922908 PMCID: PMC8146030 DOI: 10.3390/genes12050636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/02/2021] [Accepted: 04/20/2021] [Indexed: 11/17/2022] Open
Abstract
The Italian peninsula was host to a strong history of migration processes that shaped its genomic variability since prehistoric times. During the Metal Age, Sicily and Southern Italy were the protagonists of intense trade networks and settlements along the Mediterranean. Nonetheless, ancient DNA studies in Southern Italy are, at present, still limited to prehistoric and Roman Apulia. Here, we present the first mitogenomes from a Middle Bronze Age cave burial in Calabria to address this knowledge gap. We adopted a hybridization capture approach, which enabled the recovery of one complete and one partial mitochondrial genome. Phylogenetic analysis assigned these two individuals to the H1e and H5 subhaplogroups, respectively. This preliminary phylogenetic analysis supports affinities with coeval Sicilian populations, along with Linearbandkeramik and Bell Beaker cultures maternal lineages from Central Europe and Iberia. Our work represents a starting point which contributes to the comprehension of migrations and population dynamics in Southern Italy, and highlights this knowledge gap yet to be filled by genomic studies.
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Sarno S, Petrilli R, Abondio P, De Giovanni A, Boattini A, Sazzini M, De Fanti S, Cilli E, Ciani G, Gentilini D, Pettener D, Romeo G, Giuliani C, Luiselli D. Genetic history of Calabrian Greeks reveals ancient events and long term isolation in the Aspromonte area of Southern Italy. Sci Rep 2021; 11:3045. [PMID: 33542324 PMCID: PMC7862261 DOI: 10.1038/s41598-021-82591-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/15/2021] [Indexed: 01/30/2023] Open
Abstract
Calabrian Greeks are an enigmatic population that have preserved and evolved a unique variety of language, Greco, survived in the isolated Aspromonte mountain area of Southern Italy. To understand their genetic ancestry and explore possible effects of geographic and cultural isolation, we genome-wide genotyped a large set of South Italian samples including both communities that still speak Greco nowadays and those that lost the use of this language earlier in time. Comparisons with modern and ancient populations highlighted ancient, long-lasting genetic links with Eastern Mediterranean and Caucasian/Near-Eastern groups as ancestral sources of Southern Italians. Our results suggest that the Aspromonte communities might be interpreted as genetically drifted remnants that departed from such ancient genetic background as a consequence of long-term isolation. Specific patterns of population structuring and higher levels of genetic drift were indeed observed in these populations, reflecting geographic isolation amplified by cultural differences in the groups that still conserve the Greco language. Isolation and drift also affected the current genetic differentiation at specific gene pathways, prompting for future genome-wide association studies aimed at exploring trait-related loci that have drifted up in frequency in these isolated groups.
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Affiliation(s)
- Stefania Sarno
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Rosalba Petrilli
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Paolo Abondio
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Andrea De Giovanni
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Alessio Boattini
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Sazzini
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Sara De Fanti
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- grid.6292.f0000 0004 1757 1758Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Graziella Ciani
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Davide Gentilini
- grid.8982.b0000 0004 1762 5736Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy ,Italian Auxologic Institute IRCCS, Cusano Milanino, Milan, Italy
| | - Davide Pettener
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Romeo
- grid.412311.4Medical Genetics Unit, Sant’Orsola-Malpighi University Hospital, Bologna, Italy ,European School of Genetic Medicine, Bologna, Italy
| | - Cristina Giuliani
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- grid.6292.f0000 0004 1757 1758Department of Cultural Heritage, University of Bologna, Ravenna, Italy
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Birolo G, Aneli S, Di Gaetano C, Cugliari G, Russo A, Allione A, Casalone E, Giorgio E, Paraboschi EM, Ardissino D, Duga S, Asselta R, Matullo G. Functional and clinical implications of genetic structure in 1686 Italian exomes. Hum Mutat 2021; 42:272-289. [PMID: 33326653 DOI: 10.1002/humu.24156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 11/13/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
To reconstruct the phenotypical and clinical implications of the Italian genetic structure, we thoroughly analyzed a whole-exome sequencing data set comprised of 1686 healthy Italian individuals. We found six previously unreported variants with remarkable frequency differences between Northern and Southern Italy in the HERC2, OR52R1, ADH1B, and THBS4 genes. We reported 36 clinically relevant variants (submitted as pathogenic, risk factors, or drug response in ClinVar) with significant frequency differences between Italy and Europe. We then explored putatively pathogenic variants in the Italian exome. On average, our Italian individuals carried 16.6 protein-truncating variants (PTVs), with 2.5% of the population having a PTV in one of the 59 American College of Medical Genetics (ACMG) actionable genes. Lastly, we looked for PTVs that are likely to cause Mendelian diseases. We found four heterozygous PTVs in haploinsufficient genes (KAT6A, PTCH1, and STXBP1) and three homozygous PTVs in genes causing recessive diseases (DPYD, FLG, and PYGM). Comparing frequencies from our data set to other public databases, like gnomAD, we showed the importance of population-specific databases for a more accurate assessment of variant pathogenicity. For this reason, we made aggregated frequencies from our data set publicly available as a tool for both clinicians and researchers (http://nigdb.cineca.it; NIG-ExIT).
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Affiliation(s)
- Giovanni Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Serena Aneli
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | - Alessia Russo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | - Elisa Giorgio
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Elvezia M Paraboschi
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Diego Ardissino
- Division of Cardiology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
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Borg R, Farrugia Wismayer M, Bonavia K, Farrugia Wismayer A, Vella M, van Vugt JJFA, Kenna BJ, Kenna KP, Vassallo N, Veldink JH, Cauchi RJ. Genetic analysis of ALS cases in the isolated island population of Malta. Eur J Hum Genet 2021; 29:604-614. [PMID: 33414559 PMCID: PMC8115635 DOI: 10.1038/s41431-020-00767-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/16/2020] [Accepted: 10/23/2020] [Indexed: 12/11/2022] Open
Abstract
Genetic isolates are compelling tools for mapping genes of inherited disorders. The archipelago of Malta, a sovereign microstate in the south of Europe is home to a geographically and culturally isolated population. Here, we investigate the epidemiology and genetic profile of Maltese patients with amyotrophic lateral sclerosis (ALS), identified throughout a 2-year window. Cases were largely male (66.7%) with a predominant spinal onset of symptoms (70.8%). Disease onset occurred around mid-age (median age: 64 years, men; 59.5 years, female); 12.5% had familial ALS (fALS). Annual incidence rate was 2.48 (95% CI 1.59–3.68) per 100,000 person-years. Male-to-female incidence ratio was 1.93:1. Prevalence was 3.44 (95% CI 2.01–5.52) cases per 100,000 inhabitants on 31st December 2018. Whole-genome sequencing allowed us to determine rare DNA variants that change the protein-coding sequence of ALS-associated genes. Interestingly, the Maltese ALS patient cohort was found to be negative for deleterious variants in C9orf72, SOD1, TARDBP or FUS genes, which are the most commonly mutated ALS genes globally. Nonetheless, ALS-associated repeat expansions were identified in ATXN2 and NIPA1. Variants predicted to be damaging were also detected in ALS2, DAO, DCTN1, ERBB4, SETX, SCFD1 and SPG11. A total of 40% of patients with sporadic ALS had a rare and deleterious variant or repeat expansion in an ALS-associated gene, whilst the genetic cause of two thirds of fALS cases could not be pinpointed to known ALS genes or risk loci. This warrants further studies to elucidate novel genes that cause ALS in this unique population isolate.
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Affiliation(s)
- Rebecca Borg
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta.,Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Maia Farrugia Wismayer
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta.,Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Karl Bonavia
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Andrew Farrugia Wismayer
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Malcolm Vella
- Department of Neuroscience, Mater Dei Hospital, Msida, Malta
| | - Joke J F A van Vugt
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Brendan J Kenna
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kevin P Kenna
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Neville Vassallo
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta.,Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ruben J Cauchi
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta. .,Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta.
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9
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Cugliari G, Catalano C, Guarrera S, Allione A, Casalone E, Russo A, Grosso F, Ferrante D, Viberti C, Aspesi A, Sculco M, Pirazzini C, Libener R, Mirabelli D, Magnani C, Dianzani I, Matullo G. DNA Methylation of FKBP5 as Predictor of Overall Survival in Malignant Pleural Mesothelioma. Cancers (Basel) 2020; 12:cancers12113470. [PMID: 33233407 PMCID: PMC7700347 DOI: 10.3390/cancers12113470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/22/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive tumor with median survival of 12 months and limited effective treatments. The scope of this study was to study the relationship between blood DNA methylation (DNAm) and overall survival (OS) aiming at a noninvasive prognostic test. We investigated a cohort of 159 incident asbestos exposed MPM cases enrolled in an Italian area with high incidence of mesothelioma. Considering 12 months as a cut-off for OS, epigenome-wide association study (EWAS) revealed statistically significant (p value = 7.7 × 10-9) OS-related differential methylation of a single-CpG (cg03546163), located in the 5'UTR region of the FKBP5 gene. This is an independent marker of prognosis in MPM patients with a better performance than traditional inflammation-based scores such as lymphocyte-to-monocyte ratio (LMR). Cases with DNAm < 0.45 at the cg03546163 had significantly poor survival compared with those showing DNAm ≥ 0.45 (mean: 243 versus 534 days; p value< 0.001). Epigenetic changes at the FKBP5 gene were robustly associated with OS in MPM cases. Our results showed that blood DNA methylation levels could be promising and dynamic prognostic biomarkers in MPM.
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Affiliation(s)
- Giovanni Cugliari
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
- Correspondence: (G.C.); (G.M.)
| | - Chiara Catalano
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
| | - Simonetta Guarrera
- Italian Institute for Genomic Medicine, IIGM, 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Alessandra Allione
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
| | - Elisabetta Casalone
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
| | - Alessia Russo
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
| | - Federica Grosso
- Division of Medical Oncology, SS. Antonio e Biagio General Hospital, 15121 Alessandria, Italy;
| | - Daniela Ferrante
- Unit of Medical Statistics, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (D.F.); (C.M.)
- Cancer Epidemiology Unit, CPO-Piemonte, 28100 Novara, Italy
| | - Clara Viberti
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
| | - Anna Aspesi
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy; (A.A.); (M.S.); (I.D.)
| | - Marika Sculco
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy; (A.A.); (M.S.); (I.D.)
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy;
| | - Roberta Libener
- Pathology Unit, SS. Antonio e Biagio General Hospital, 15122 Alessandria, Italy;
| | - Dario Mirabelli
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, 10126 Turin, Italy;
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates “G. Scansetti”, University of Turin, 10126 Turin, Italy
| | - Corrado Magnani
- Unit of Medical Statistics, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (D.F.); (C.M.)
- Cancer Epidemiology Unit, CPO-Piemonte, 28100 Novara, Italy
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates “G. Scansetti”, University of Turin, 10126 Turin, Italy
| | - Irma Dianzani
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy; (A.A.); (M.S.); (I.D.)
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates “G. Scansetti”, University of Turin, 10126 Turin, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (A.A.); (E.C.); (A.R.); (C.V.)
- Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates “G. Scansetti”, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, AOU Città della Salute e della Scienza, 10126 Turin, Italy
- Correspondence: (G.C.); (G.M.)
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10
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Piras IS, Picinelli C, Iennaco R, Baccarin M, Castronovo P, Tomaiuolo P, Cucinotta F, Ricciardello A, Turriziani L, Nanetti L, Mariotti C, Gellera C, Lintas C, Sacco R, Zuccato C, Cattaneo E, Persico AM. Huntingtin gene CAG repeat size affects autism risk: Family-based and case-control association study. Am J Med Genet B Neuropsychiatr Genet 2020; 183:341-351. [PMID: 32652810 DOI: 10.1002/ajmg.b.32806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/20/2020] [Accepted: 05/04/2020] [Indexed: 11/10/2022]
Abstract
The Huntingtin (HTT) gene contains a CAG repeat in exon 1, whose expansion beyond 39 repeats consistently leads to Huntington's disease (HD), whereas normal-to-intermediate alleles seemingly modulate brain structure, function and behavior. The role of the CAG repeat in Autism Spectrum Disorder (ASD) was investigated applying both family-based and case-control association designs, with the SCA3 repeat as a negative control. Significant overtransmission of "long" CAG alleles (≥17 repeats) to autistic children and of "short" alleles (≤16 repeats) to their unaffected siblings (all p < 10-5 ) was observed in 612 ASD families (548 simplex and 64 multiplex). Surprisingly, both 193 population controls and 1,188 neurological non-HD controls have significantly lower frequencies of "short" CAG alleles compared to 185 unaffected siblings and higher rates of "long" alleles compared to 548 ASD patients from the same families (p < .05-.001). The SCA3 CAG repeat displays no association. "Short" HTT alleles seemingly exert a protective effect from clinically overt autism in families carrying a genetic predisposition for ASD, while "long" alleles may enhance autism risk. Differential penetrance of autism-inducing genetic/epigenetic variants may imply atypical developmental trajectories linked to HTT functions, including excitation/inhibition imbalance, cortical neurogenesis and apoptosis, neuronal migration, synapse formation, connectivity and homeostasis.
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Affiliation(s)
- Ignazio Stefano Piras
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Chiara Picinelli
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Raffaele Iennaco
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy.,Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Marco Baccarin
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Paola Castronovo
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Pasquale Tomaiuolo
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Francesca Cucinotta
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Arianna Ricciardello
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Laura Turriziani
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Lorenzo Nanetti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Caterina Mariotti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Carla Lintas
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University Campus Bio-Medico, Rome, Italy
| | - Roberto Sacco
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University Campus Bio-Medico, Rome, Italy
| | - Chiara Zuccato
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy.,Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Elena Cattaneo
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy.,Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Antonio M Persico
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
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11
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Modi A, Lancioni H, Cardinali I, Capodiferro MR, Rambaldi Migliore N, Hussein A, Strobl C, Bodner M, Schnaller L, Xavier C, Rizzi E, Bonomi Ponzi L, Vai S, Raveane A, Cavadas B, Semino O, Torroni A, Olivieri A, Lari M, Pereira L, Parson W, Caramelli D, Achilli A. The mitogenome portrait of Umbria in Central Italy as depicted by contemporary inhabitants and pre-Roman remains. Sci Rep 2020; 10:10700. [PMID: 32612271 PMCID: PMC7329865 DOI: 10.1038/s41598-020-67445-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/22/2020] [Indexed: 12/19/2022] Open
Abstract
Umbria is located in Central Italy and took the name from its ancient inhabitants, the Umbri, whose origins are still debated. Here, we investigated the mitochondrial DNA (mtDNA) variation of 545 present-day Umbrians (with 198 entire mitogenomes) and 28 pre-Roman individuals (obtaining 19 ancient mtDNAs) excavated from the necropolis of Plestia. We found a rather homogeneous distribution of western Eurasian lineages across the region, with few notable exceptions. Contemporary inhabitants of the eastern part, delimited by the Tiber River and the Apennine Mountains, manifest a peculiar mitochondrial proximity to central-eastern Europeans, mainly due to haplogroups U4 and U5a, and an overrepresentation of J (30%) similar to the pre-Roman remains, also excavated in East Umbria. Local genetic continuities are further attested to by six terminal branches (H1e1, J1c3, J2b1, U2e2a, U8b1b1 and K1a4a) shared between ancient and modern mitogenomes. Eventually, we identified multiple inputs from various population sources that likely shaped the mitochondrial gene pool of ancient Umbri over time, since early Neolithic, including gene flows with central-eastern Europe. This diachronic mtDNA portrait of Umbria fits well with the genome-wide population structure identified on the entire peninsula and with historical sources that list the Umbri among the most ancient Italic populations.
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Affiliation(s)
- Alessandra Modi
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123, Perugia, Italy.
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123, Perugia, Italy
| | - Marco R Capodiferro
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Abir Hussein
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Lisa Schnaller
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, CNR, Segrate, 20090, Milan, Italy
| | | | - Stefania Vai
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Bruno Cavadas
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal.,i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200-135, Porto, Portugal
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Martina Lari
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Luisa Pereira
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal.,i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200-135, Porto, Portugal
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, PA, 16801, USA
| | - David Caramelli
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy.
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12
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Tait S, Carli F, Busani L, Buzzigoli E, Della Latta V, Deodati A, Fabbrizi E, Gaggini M, Maranghi F, Tassinari R, Toffol G, Cianfarani S, Gastaldelli A, La Rocca C. Biomonitoring of Bis(2-ethylhexyl)phthalate (DEHP) in Italian children and adolescents: Data from LIFE PERSUADED project. ENVIRONMENTAL RESEARCH 2020; 185:109428. [PMID: 32251910 DOI: 10.1016/j.envres.2020.109428] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/24/2020] [Accepted: 03/22/2020] [Indexed: 06/11/2023]
Abstract
The Bis(2-ethylhexyl)phthalate (DEHP), a widespread plasticizer, is considered an endocrine disrupting chemical with main toxicological effects on reproductive and metabolic systems. Human biomonitoring (HBM) studies are promoted to evaluate the background exposure levels. In the frame of LIFE PERSUADED project, the HBM study measured DEHP main metabolites (mono-(2-ethylhexyl) phthalate, MEHP; 2-ethyl-5-hydroxy-hexylphthalate, MEHHP; 2-ethyl-5-oxo-hexylphthalate, MEOHP) in Italian children and adolescent (4-14 years old) according to geographical macro-areas and areas, age and sex. Children from the South and the Centre of Italy showed higher median levels of DEHP, as a sum of its metabolites (48.14 and 47.80 μg/L), than those from the North (39.47 μg/L; p = 0.0090 and 0.0004, respectively). Considering the total population, boys are more exposed than girls (only as urinary volume), and children aged 4-6 years have higher median levels than those 7-10 and 11-14 years old. The derived reference values (RV95) for DEHP in children is 168 μg/L. The relative metabolic rates of DEHP, the background levels and, thus, the RV95, vary with the geographical area, age and sex, indicating that all these parameters should be considered in the risk assessment.
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Affiliation(s)
- Sabrina Tait
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Fabrizia Carli
- Institute of Clinical Physiology, National Research Council, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Luca Busani
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Emma Buzzigoli
- Institute of Clinical Physiology, National Research Council, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Veronica Della Latta
- Institute of Clinical Physiology, National Research Council, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Annalisa Deodati
- Dipartimento Pediatrico Universitario Ospedaliero "Bambino Gesù" Children's Hospital, Piazza di Sant'Onofrio 4, 00165, Rome, Italy.
| | - Enrica Fabbrizi
- Unità Operativa Complessa Pediatria e Neonatologia, Augusto Murri Hospital, Via Augusto Murri 21, 63900, Fermo, Italy.
| | - Melania Gaggini
- Institute of Clinical Physiology, National Research Council, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Francesca Maranghi
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Roberta Tassinari
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Giacomo Toffol
- Associazione Culturale Pediatri, Via Montiferru 6, 09070, Narbolia (OR), Italy.
| | - Stefano Cianfarani
- Dipartimento Pediatrico Universitario Ospedaliero "Bambino Gesù" Children's Hospital, Piazza di Sant'Onofrio 4, 00165, Rome, Italy; University of Rome Tor Vergata, Via Cracovia, 50, 00133, Rome, Italy; Department of Women's and Children's Health, Karolinska Institutet and University Hospital, Solnavägen 1, 171 77, Solna, Stockholm, Sweden.
| | - Amalia Gastaldelli
- Institute of Clinical Physiology, National Research Council, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Cinzia La Rocca
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
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13
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Palumbo S, Mariotti V, Anastasio T, Rota G, Lucchi L, Manfrinati A, Rumiati R, Lotto L, Sarlo M, Pietrini P, Pellegrini S. A genetic profile of oxytocin receptor improves moral acceptability of outcome-maximizing harm in male insurance brokers. Behav Brain Res 2020; 392:112681. [PMID: 32387223 DOI: 10.1016/j.bbr.2020.112681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/26/2020] [Accepted: 04/27/2020] [Indexed: 11/30/2022]
Abstract
In recent years, conflicting findings have been reported in the scientific literature about the influence of dopaminergic, serotonergic and oxytocinergic gene variants on moral behavior. Here, we utilized a moral judgment paradigm to test the potential effects on moral choices of three polymorphisms of the Oxytocin receptor (OXTR): rs53576, rs2268498 and rs1042770. We analyzed the influence of each single polymorphism and of genetic profiles obtained by different combinations of their genotypes in a sample of male insurance brokers (n = 129), as compared to control males (n = 109). Insurance brokers resulted significantly more oriented to maximize outcomes than control males, thus they expressed more than controls the utilitarian attitude phenotype. When analyzed individually, none of the selected variants influenced the responses to moral dilemmas. In contrast, a composite genetic profile that potentially increases OXTR activity was associated with higher moral acceptability in brokers. We hypothesize that this genetic profile promotes outcome-maximizing behavior in brokers by focusing their attention on what represents a greater good, that is, saving the highest number of people, even though at the cost of sacrificing one individual. Our data suggest that investigations in a sample that most expresses the phenotype of interest, combined with the analysis of composite genetic profiles rather than individual variants, represent a promising strategy to find out weak genetic influences on complex phenotypes, such as moral behavior.
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Affiliation(s)
- Sara Palumbo
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Pisa, Italy
| | - Veronica Mariotti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Teresa Anastasio
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | | | - Andrea Manfrinati
- Department of Developmental Psychology and Socialization, University of Padova, Padova, Italy
| | - Rino Rumiati
- Department of Developmental Psychology and Socialization, University of Padova, Padova, Italy
| | - Lorella Lotto
- Department of Developmental Psychology and Socialization, University of Padova, Padova, Italy
| | - Michela Sarlo
- Department of General Psychology and Padova Neuroscience Center, University of Padova, Padova, Italy
| | | | - Silvia Pellegrini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.
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14
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Puoti C. COVID: How to explain differences in lethality between different populations? Med Hypotheses 2020; 140:109784. [PMID: 32361101 DOI: 10.1016/j.mehy.2020.109784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022]
Affiliation(s)
- Claudio Puoti
- INI Research Institute and Clinics, Grottaferrata, Rome, Italy.
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15
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Mirabelli M, Chiefari E, Caroleo P, Arcidiacono B, Corigliano DM, Giuliano S, Brunetti FS, Tanyolaç S, Foti DP, Puccio L, Brunetti A. Long-Term Effectiveness of Liraglutide for Weight Management and Glycemic Control in Type 2 Diabetes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 17:ijerph17010207. [PMID: 31892206 PMCID: PMC6981922 DOI: 10.3390/ijerph17010207] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/17/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022]
Abstract
Background: Liraglutide is the first glucagon-like peptide-1 receptor agonist (GLP-1 RA) based on the human GLP-1 sequence, with potential weight loss benefits, approved for the treatment of type 2 diabetes (T2D) mellitus. Herein, we aimed to assess the 5-year effectiveness of Liraglutide in the management of weight and glycometabolic control in a Southern Italian cohort of overweight/obese T2D patients, who were naïve to GLP-1 RAs. Patients and Methods: Forty overweight or obese patients treated with Liraglutide at doses up to 1.8 mg/day, in combination with one or more oral antidiabetic agents, were retrospectively assessed at baseline, during, and after 60 months of continuous therapy. Results: After 5 years of Liraglutide treatment, body weight decreased from 92.1 ± 20.5 kg to 87.3 ± 20.0 Kg (p < 0.001), with a mean reduction of 5.0 ± 7.0 Kg and a body mass index (BMI) decrement of −2.0 ± 3.1 Kg/m2. On Spearman’s univariate analysis, change in body weight was correlated with female gender and baseline BMI. Hemoglobin A1c (HbA1c) decreased from 7.9 ± 0.9% at baseline to 7.0 ± 0.7% at the end of the study period (p < 0.001), followed by a significant reduction in fasting plasma glucose. No significant differences emerged in other biochemical parameters, despite a trend toward improvement in lipid profile. Notwithstanding encouraging effects on several markers of cardiovascular disease (CVD), increments in the 5- and 10-year risk for the first atherosclerotic cardiovascular event were documented, as four incident cases of myocardial infarction. Conclusions: Prolonging treatment with Liraglutide can lead to durable benefits in relation to weight and glycemic control, with a greater impact on women. These results extend and corroborate previous observations, suggesting that gender per se may modulate the response to Liraglutide. Despite favorable effects on some established CVD risks factors, the long-term role of Liraglutide in primary prevention of CVD in patients with T2D remains controversial.
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Affiliation(s)
- Maria Mirabelli
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy; (M.M.); (E.C.); (B.A.); (D.M.C.); (S.G.); (F.S.B.); (D.P.F.)
| | - Eusebio Chiefari
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy; (M.M.); (E.C.); (B.A.); (D.M.C.); (S.G.); (F.S.B.); (D.P.F.)
| | - Patrizia Caroleo
- Complex Operative Structure Endocrinology-Diabetology, Hospital Pugliese-Ciaccio, 88100 Catanzaro, Italy; (P.C.); (L.P.)
| | - Biagio Arcidiacono
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy; (M.M.); (E.C.); (B.A.); (D.M.C.); (S.G.); (F.S.B.); (D.P.F.)
| | - Domenica Maria Corigliano
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy; (M.M.); (E.C.); (B.A.); (D.M.C.); (S.G.); (F.S.B.); (D.P.F.)
| | - Stefania Giuliano
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy; (M.M.); (E.C.); (B.A.); (D.M.C.); (S.G.); (F.S.B.); (D.P.F.)
| | - Francesco Saverio Brunetti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy; (M.M.); (E.C.); (B.A.); (D.M.C.); (S.G.); (F.S.B.); (D.P.F.)
| | - Sinan Tanyolaç
- Division of Endocrinology and Metabolism, Department of Internal Medicine, School of Medicine, Biruni University, 34010 Istanbul, Turkey;
| | - Daniela Patrizia Foti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy; (M.M.); (E.C.); (B.A.); (D.M.C.); (S.G.); (F.S.B.); (D.P.F.)
| | - Luigi Puccio
- Complex Operative Structure Endocrinology-Diabetology, Hospital Pugliese-Ciaccio, 88100 Catanzaro, Italy; (P.C.); (L.P.)
| | - Antonio Brunetti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy; (M.M.); (E.C.); (B.A.); (D.M.C.); (S.G.); (F.S.B.); (D.P.F.)
- Correspondence: ; Tel.: +39-0961-3694368; Fax: +39-0961-3694147
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16
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Grugni V, Raveane A, Colombo G, Nici C, Crobu F, Ongaro L, Battaglia V, Sanna D, Al-Zahery N, Fiorani O, Lisa A, Ferretti L, Achilli A, Olivieri A, Francalacci P, Piazza A, Torroni A, Semino O. Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case. Int J Mol Sci 2019; 20:E5763. [PMID: 31744094 PMCID: PMC6888588 DOI: 10.3390/ijms20225763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 11/17/2022] Open
Abstract
Many anthropological, linguistic, genetic and genomic analyses have been carried out to evaluate the potential impact that evolutionary forces had in shaping the present-day Sardinian gene pool, the main outlier in the genetic landscape of Europe. However, due to the homogenizing effect of internal movements, which have intensified over the past fifty years, only partial information has been obtained about the main demographic events. To overcome this limitation, we analyzed the male-specific region of the Y chromosome in three population samples obtained by reallocating a large number of Sardinian subjects to the place of origin of their monophyletic surnames, which are paternally transmitted through generations in most of the populations, much like the Y chromosome. Three Y-chromosome founding lineages, G2-L91, I2-M26 and R1b-V88, were identified as strongly contributing to the definition of the outlying position of Sardinians in the European genetic context and marking a significant differentiation within the island. The present distribution of these lineages does not always mirror that detected in ancient DNAs. Our results show that the analysis of the Y-chromosome gene pool coupled with a sampling method based on the origin of the family name, is an efficient approach to unravelling past heterogeneity, often hidden by recent movements, in the gene pool of modern populations. Furthermore, the reconstruction and comparison of past genetic isolates represent a starting point to better assess the genetic information deriving from the increasing number of available ancient DNA samples.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Carmen Nici
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Francesca Crobu
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Italy
| | - Linda Ongaro
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Estonian Biocentre, Institute of Genomics, Riia 23, 51010 Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, 51010 Tartu, Estonia
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Daria Sanna
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy
| | - Nadia Al-Zahery
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Ornella Fiorani
- Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; (O.F.); (A.L.)
| | - Antonella Lisa
- Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; (O.F.); (A.L.)
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Paolo Francalacci
- Dipartimento di Scienza della Vita e dell’Ambiente, Università di Cagliari, 09123 Cagliari, Italy;
| | - Alberto Piazza
- Dipartimento di Scienze Mediche, Scuola di Medicina, Università di Torino, 10124 Torino, Italy;
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
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Sanghera DK, Bejar C, Sapkota B, Wander GS, Ralhan S. Frequencies of poor metabolizer alleles of 12 pharmacogenomic actionable genes in Punjabi Sikhs of Indian Origin. Sci Rep 2018; 8:15742. [PMID: 30356105 PMCID: PMC6200732 DOI: 10.1038/s41598-018-33981-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 09/28/2018] [Indexed: 12/28/2022] Open
Abstract
Diversity in drug response is attributed to both genetic and non-genetic factors. However, there is paucity of pharmacogenetics information across ethnically and genetically diverse populations of India. Here, we have analyzed 21 SNPs from 12 pharmacogenomics genes in Punjabi Sikhs of Indian origin (N = 1,616), as part of the Sikh Diabetes Study (SDS). We compared the allele frequency of poor metabolism (PM) phenotype among Sikhs across other major global populations from the Exome Aggregation Consortium and 1000 Genomes. The PM phenotype of CYP1A2*1 F for slow metabolism of caffeine and carcinogens was significantly higher in Indians (SDS 42%, GIH [Gujarati] 51%, SAS [Pakistani] 45%) compared to Europeans 29% (pgenotype = 5.3E-05). Similarly, South Asians had a significantly higher frequency of CYP2C9*3 (12% SDS, 13% GIH, 11% SAS) vs. 7% in Europeans (pgenotype = <1.0E-05) and ‘T’ allele of CYP4F2 (36%) SDS, (43%) GIH, 40% (SAS) vs. (29%) in Europeans (pgenotype = <1.0E-05); both associated with a higher risk of bleeding with warfarin. All South Asians –the Sikhs (0.36), GIH (0.34), and SAS (0.36) had a higher frequency of the NAT2*6 allele (linked with slow acetylation of isoniazid) compared to Europeans (0.29). Additionally, the prevalence of the low activity ‘C’ allele of MTHFR (rs1801131) was highest in Sikhs compared to all other ethnic groups [SDS (44%), GIH (39%), SAS (42%) and European (32%) (pgenotype = <1.0E-05)]. SNPs in MTHFR affect metabolism of statins, 5-fluorouracil and methotrexate-based cancer drugs. These findings underscore the need for evaluation of other endogamous ethnic groups of India and beyond for establishing a global benchmark for pre-emptive genotyping in drug metabolizing genes before beginning therapeutic intervention.
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Affiliation(s)
- Dharambir K Sanghera
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. .,Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Cynthia Bejar
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Bishwa Sapkota
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | - Sarju Ralhan
- Hero DMC Heart Institute, Ludhiana, Punjab, India
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18
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Serventi P, Panicucci C, Bodega R, De Fanti S, Sarno S, Fondevila Alvarez M, Brisighelli F, Trombetta B, Anagnostou P, Ferri G, Vazzana A, Delpino C, Gruppioni G, Luiselli D, Cilli E. Iron Age Italic population genetics: the Piceni from Novilara (8th-7th century BC). Ann Hum Biol 2018; 45:34-43. [PMID: 29216758 DOI: 10.1080/03014460.2017.1414876] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed. AIMS To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis. SUBJECTS AND METHODS In a first set of 10 individuals from Novilara, we performed deep sequencing of the HVS-I region of the mtDNA, combined with the genotyping of 22 SNPs in the coding region and the analysis of several autosomal markers. RESULTS The results show a low nucleotide diversity for the inhabitants of Novilara and highlight a genetic affinity of this ancient population with the current inhabitants of central Italy. No family relationship was observed between the individuals analysed here. CONCLUSIONS This study provides a preliminary characterisation of the mtDNA variability of the Piceni of Novilara, as well as a kinship assessment of two peculiar burials.
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Affiliation(s)
- Patrizia Serventi
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy.,b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Chiara Panicucci
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Roberta Bodega
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Sara De Fanti
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Stefania Sarno
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Manuel Fondevila Alvarez
- c Instituto de Ciencias Forenses 'Luis Concheiro' , University of Santiago de Compostela, Santiago de Compostela , Galicia , Spain
| | - Francesca Brisighelli
- d Sezione di Medicina Legale-Istituto di Sanità Pubblica , Università Cattolica del Sacro Cuore , Roma , Italy
| | - Beniamino Trombetta
- e Department of Biology and Biotechnology 'Charles Darwin' , Sapienza University , Rome , Italy
| | - Paolo Anagnostou
- f Department of Environmental Biology , University of Rome 'La Sapienza' , Rome , Italy.,g ISItA, Istituto Italiano di Antropologia , Rome , Italy
| | - Gianmarco Ferri
- h Department of Diagnostic and Clinical Medicine and Public Health , University of Modena and Reggio Emilia , Modena , Italy
| | - Antonino Vazzana
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Chiara Delpino
- i Superintendence of Archaeological Heritage of Marche Region , Ancona , Italy
| | - Giorgio Gruppioni
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Donata Luiselli
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Elisabetta Cilli
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
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19
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Boattini A, Sarno S, Fiorani O, Lisa A, Luiselli D, Pettener D. Ripples on the surface. Surnames and genes in Sicily and Southern Italy. Ann Hum Biol 2018; 45:57-65. [PMID: 29183201 DOI: 10.1080/03014460.2017.1411525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Southern Italy and Sicily played a key role in the peopling history of the Mediterranean. While genetic research showed the remarkable homogeneity of these regions, surname-based studies instead suggested low population mobility, hence potential structuring. AIM In order to better understand these different patterns, this study (1) thoroughly analysed the surname structure of Sicily and Southern Italy and (2) tested its relationships with a wide set of molecular markers. SUBJECTS AND METHODS Surname data were collected from 1213 municipalities and compared to uniparental and autosomal genetic markers typed in ∼300 individuals from 8-10 populations. Surname analyses were performed using different multivariate methods, while comparisons with genetic data relied on correlation tests. RESULTS Surnames were clearly structured according to regional geographic patterns, which likely emerged because of recent isolation-by-distance-like population dynamics. In general, genetic markers, hinting at a pervasive homogeneity, did not correlate with surname distribution. However, long autosomal haplotypes (>5 cM) that compared to genotypic (SNPs) data identify more "recent" relatedness, showing a clear association with surname patterns. CONCLUSION The apparent contradiction between surname structure and genetic homogeneity was resolved by figuring surnames as recent "ripples" deposited on a vast and ancient homogeneous genetic "surface".
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Affiliation(s)
- Alessio Boattini
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Stefania Sarno
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Ornella Fiorani
- b Institute of Molecular Genetics (IGM) , Consiglio Nazionale delle Ricerche (CNR) , Pavia , Italy
| | - Antonella Lisa
- b Institute of Molecular Genetics (IGM) , Consiglio Nazionale delle Ricerche (CNR) , Pavia , Italy
| | - Donata Luiselli
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Davide Pettener
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
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20
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A finely resolved phylogeny of Y chromosome Hg J illuminates the processes of Phoenician and Greek colonizations in the Mediterranean. Sci Rep 2018; 8:7465. [PMID: 29748665 PMCID: PMC5945646 DOI: 10.1038/s41598-018-25912-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/25/2018] [Indexed: 11/15/2022] Open
Abstract
In order to improve the phylogeography of the male-specific genetic traces of Greek and Phoenician colonizations on the Northern coasts of the Mediterranean, we performed a geographically structured sampling of seven subclades of haplogroup J in Turkey, Greece and Italy. We resequenced 4.4 Mb of Y-chromosome in 58 subjects, obtaining 1079 high quality variants. We did not find a preferential coalescence of Turkish samples to ancestral nodes, contradicting the simplistic idea of a dispersal and radiation of Hg J as a whole from the Middle East. Upon calibration with an ancient Hg J chromosome, we confirmed that signs of Holocenic Hg J radiations are subtle and date mainly to the Bronze Age. We pinpointed seven variants which could potentially unveil star clusters of sequences, indicative of local expansions. By directly genotyping these variants in Hg J carriers and complementing with published resequenced chromosomes (893 subjects), we provide strong temporal and distributional evidence for markers of the Greek settlement of Magna Graecia (J2a-L397) and Phoenician migrations (rs760148062). Our work generated a minimal but robust list of evolutionarily stable markers to elucidate the demographic dynamics and spatial domains of male-mediated movements across and around the Mediterranean, in the last 6,000 years.
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21
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Robino C, Lacerenza D, Aneli S, Di Gaetano C, Matullo G, Robledo R, Calò C. Allele and haplotype diversity of 12 X-STRs in Sardinia. Forensic Sci Int Genet 2017; 33:e1-e3. [PMID: 29221994 DOI: 10.1016/j.fsigen.2017.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/11/2017] [Accepted: 12/02/2017] [Indexed: 11/27/2022]
Abstract
The analysis of clusters of tightly linked X-chromosome short tandem repeat (STR) markers can assist the interpretation of complex kinship cases. However, when linkage disequilibrium (LD) is present in the population of origin of tested individuals, haplotype rather than allele frequencies should be used in likelihood calculations. The diversity of twelve X-STRs arranged in four linkage groups (I: DXS10148-DXS10135-DXS8378; II: DXS7132-DXS10079-DXS10074; III: DXS10103-HPRTB-DXS10101; IV: DXS10146-DXS10134-DXS7423) was tested in a Sardinian population sample (n=516) including three open populations from the Northern, Central and Southern part of the island, and three isolates (Benetutti, Desulo, Carloforte). Evidence of LD was detected in Sardinia within each linkage group. Significant differences in haplotype and allele frequency distribution of X-STR markers was seen between isolates and open populations, which on the contrary appeared highly homogeneous. The percentage of Sardinian haplotypes previously unobserved in a similar dataset compiled for the Italian population was: 76.3% (linkage group I), 61.3% (linkage group II), 54.1% (linkage group III), 58.9% (linkage group IV). Significant pairwise genetic differences were seen between mainland Italy, the three Sardinian isolates, and the open population of Southern Sardinia. The study confirms the presence of high levels and complex patterns of LD along the X chromosome in Sardinia, and provides population-specific haplotype data for biostatistical evaluation in kinship testing.
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Affiliation(s)
- C Robino
- Dipartimento di Scienze della Sanità Pubblica e Pediatriche, Università di Torino, Italy.
| | - D Lacerenza
- Dipartimento di Scienze della Sanità Pubblica e Pediatriche, Università di Torino, Italy
| | - S Aneli
- Dipartimento di Scienze Mediche, Università di Torino, Italy; Italian Institute of Genomic Medicine, Torino, Italy
| | - C Di Gaetano
- Dipartimento di Scienze Mediche, Università di Torino, Italy; Italian Institute of Genomic Medicine, Torino, Italy
| | - G Matullo
- Dipartimento di Scienze Mediche, Università di Torino, Italy; Italian Institute of Genomic Medicine, Torino, Italy
| | - R Robledo
- Dipartimento di Scienze Biomediche, Università di Cagliari, Italy
| | - C Calò
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Italy
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22
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Pellegrini S, Palumbo S, Iofrida C, Melissari E, Rota G, Mariotti V, Anastasio T, Manfrinati A, Rumiati R, Lotto L, Sarlo M, Pietrini P. Genetically-Driven Enhancement of Dopaminergic Transmission Affects Moral Acceptability in Females but Not in Males: A Pilot Study. Front Behav Neurosci 2017; 11:156. [PMID: 28900390 PMCID: PMC5581873 DOI: 10.3389/fnbeh.2017.00156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/08/2017] [Indexed: 11/13/2022] Open
Abstract
Moral behavior has been a key topic of debate for philosophy and psychology for a long time. In recent years, thanks to the development of novel methodologies in cognitive sciences, the question of how we make moral choices has expanded to the study of neurobiological correlates that subtend the mental processes involved in moral behavior. For instance, in vivo brain imaging studies have shown that distinct patterns of brain neural activity, associated with emotional response and cognitive processes, are involved in moral judgment. Moreover, while it is well-known that responses to the same moral dilemmas differ across individuals, to what extent this variability may be rooted in genetics still remains to be understood. As dopamine is a key modulator of neural processes underlying executive functions, we questioned whether genetic polymorphisms associated with decision-making and dopaminergic neurotransmission modulation would contribute to the observed variability in moral judgment. To this aim, we genotyped five genetic variants of the dopaminergic pathway [rs1800955 in the dopamine receptor D4 (DRD4) gene, DRD4 48 bp variable number of tandem repeat (VNTR), solute carrier family 6 member 3 (SLC6A3) 40 bp VNTR, rs4680 in the catechol-O-methyl transferase (COMT) gene, and rs1800497 in the ankyrin repeat and kinase domain containing 1 (ANKK1) gene] in 200 subjects, who were requested to answer 56 moral dilemmas. As these variants are all located in genes belonging to the dopaminergic pathway, they were combined in multilocus genetic profiles for the association analysis. While no individual variant showed any significant effects on moral dilemma responses, the multilocus genetic profile analysis revealed a significant gender-specific influence on human moral acceptability. Specifically, those genotype combinations that improve dopaminergic signaling selectively increased moral acceptability in females, by making their responses to moral dilemmas more similar to those provided by males. As females usually give more emotionally-based answers and engage the "emotional brain" more than males, our results, though preliminary and therefore in need of replication in independent samples, suggest that this increase in dopamine availability enhances the cognitive and reduces the emotional components of moral decision-making in females, thus favoring a more rationally-driven decision process.
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Affiliation(s)
- Silvia Pellegrini
- Department of Experimental and Clinical Medicine, University of PisaPisa, Italy
| | - Sara Palumbo
- Department of Surgical, Medical, Molecular Pathology and Critical Care, University of PisaPisa, Italy
| | | | - Erika Melissari
- Department of Surgical, Medical, Molecular Pathology and Critical Care, University of PisaPisa, Italy
| | - Giuseppina Rota
- Clinical Psychology Branch, Azienda Ospedaliero-Universitaria PisanaPisa, Italy
| | - Veronica Mariotti
- Department of Experimental and Clinical Medicine, University of PisaPisa, Italy
| | - Teresa Anastasio
- Department of Experimental and Clinical Medicine, University of PisaPisa, Italy
| | - Andrea Manfrinati
- Applied Research Division for Cognitive and Psychological Science, European Institute of OncologyMilan, Italy
| | - Rino Rumiati
- Department of Developmental Psychology and Socialization and Center for Cognitive Neuroscience, University of PadovaPadova, Italy
| | - Lorella Lotto
- Department of Developmental Psychology and Socialization and Center for Cognitive Neuroscience, University of PadovaPadova, Italy
| | - Michela Sarlo
- Department of General Psychology and Center for Cognitive Neuroscience, University of PadovaPadova, Italy
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Santovito A, Gendusa C, Matini A, Ferraro F, Musso I, Costanzo M, Delclos A, Cervella P. Frequency distribution of six cytokine gene polymorphisms in North- and South-Italy. Int J Immunogenet 2017; 44:158-163. [DOI: 10.1111/iji.12324] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/10/2017] [Accepted: 04/20/2017] [Indexed: 01/22/2023]
Affiliation(s)
- A. Santovito
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - C. Gendusa
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - A. Matini
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - F. Ferraro
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - I. Musso
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - M. Costanzo
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - A. Delclos
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - P. Cervella
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
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24
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Ancient and recent admixture layers in Sicily and Southern Italy trace multiple migration routes along the Mediterranean. Sci Rep 2017; 7:1984. [PMID: 28512355 PMCID: PMC5434004 DOI: 10.1038/s41598-017-01802-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/04/2017] [Indexed: 12/12/2022] Open
Abstract
The Mediterranean shores stretching between Sicily, Southern Italy and the Southern Balkans witnessed a long series of migration processes and cultural exchanges. Accordingly, present-day population diversity is composed by multiple genetic layers, which make the deciphering of different ancestral and historical contributes particularly challenging. We address this issue by genotyping 511 samples from 23 populations of Sicily, Southern Italy, Greece and Albania with the Illumina GenoChip Array, also including new samples from Albanian- and Greek-speaking ethno-linguistic minorities of Southern Italy. Our results reveal a shared Mediterranean genetic continuity, extending from Sicily to Cyprus, where Southern Italian populations appear genetically closer to Greek-speaking islands than to continental Greece. Besides a predominant Neolithic background, we identify traces of Post-Neolithic Levantine- and Caucasus-related ancestries, compatible with maritime Bronze-Age migrations. We argue that these results may have important implications in the cultural history of Europe, such as in the diffusion of some Indo-European languages. Instead, recent historical expansions from North-Eastern Europe account for the observed differentiation of present-day continental Southern Balkan groups. Patterns of IBD-sharing directly reconnect Albanian-speaking Arbereshe with a recent Balkan-source origin, while Greek-speaking communities of Southern Italy cluster with their Italian-speaking neighbours suggesting a long-term history of presence in Southern Italy.
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25
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Chiefari E, Ventura V, Capula C, Randazzo G, Scorcia V, Fedele M, Arcidiacono B, Nevolo MT, Bilotta FL, Vitiello M, Palmieri C, Gulletta E, Fusco A, Foti D, Vero R, Brunetti A. A polymorphism of HMGA1 protects against proliferative diabetic retinopathy by impairing HMGA1-induced VEGFA expression. Sci Rep 2016; 6:39429. [PMID: 27991577 PMCID: PMC5171873 DOI: 10.1038/srep39429] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/22/2016] [Indexed: 12/18/2022] Open
Abstract
Diabetic retinopathy (DR) is a major complication of diabetes mellitus, and is the leading cause of blindness in working-age people. Usually, DR progresses from the asymptomatic non-proliferative DR that does not significantly alter vision, to proliferative DR (PDR), which can result in aberrant retinal neovessel formation and blindness. The High-Mobility-Group A1 (HMGA1) protein is a transcriptional master regulator of numerous genes, including metabolic and inflammatory genes, which, by modulating the expression of angiogenic factors, may induce retinal neovascularization, a hallmark of PDR. Herein, we examined the relationship between HMGA1 rs139876191 variant and DR. Results revealed that patients with type 2 diabetes, who were carriers of the HMGA1 rs139876191 variant had a significantly lower risk of developing PDR, compared to non-carrier diabetic patients. From a mechanistic point of view, our findings indicated that, by adversely affecting HMGA1 protein expression and function, the HMGA1 rs139876191 variant played a key role in this protective mechanism by downregulating the expression of vascular endothelial growth factor A (VEGFA), a major activator of neovascularization in DR. These data provide new insights into the pathogenesis and progression of DR, and may offer opportunities for discovering novel biomarkers and therapeutic targets for diagnosis, prevention and treatment of PDR.
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Affiliation(s)
- Eusebio Chiefari
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Valeria Ventura
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Carmelo Capula
- Operative Unit of Endocrinology and Diabetes, Hospital Pugliese-Ciaccio, Catanzaro, Italy
| | - Giorgio Randazzo
- Department of Clinical and Experimental Medicine, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Vincenzo Scorcia
- Department of Clinical and Experimental Medicine, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Monica Fedele
- Institute of Experimental Endocrinology and Oncology, CNR, Napoli, Italy
| | - Biagio Arcidiacono
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Maria Teresa Nevolo
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | | | - Michela Vitiello
- Institute of Experimental Endocrinology and Oncology, CNR, Napoli, Italy
| | - Camillo Palmieri
- Department of Clinical and Experimental Medicine, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Elio Gulletta
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Alfredo Fusco
- Institute of Experimental Endocrinology and Oncology, CNR, Napoli, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, Napoli, Italy
| | - Daniela Foti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Raffaella Vero
- Operative Unit of Endocrinology and Diabetes, Hospital Pugliese-Ciaccio, Catanzaro, Italy
| | - Antonio Brunetti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
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Messina F, Finocchio A, Akar N, Loutradis A, Michalodimitrakis EI, Brdicka R, Jodice C, Novelletto A. Spatially Explicit Models to Investigate Geographic Patterns in the Distribution of Forensic STRs: Application to the North-Eastern Mediterranean. PLoS One 2016; 11:e0167065. [PMID: 27898725 PMCID: PMC5127579 DOI: 10.1371/journal.pone.0167065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/08/2016] [Indexed: 11/18/2022] Open
Abstract
Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies. Using spatial PCA on the full dataset, we detected patterns of population affinities in the area. Additionally, we devised objective criteria to reduce the overall complexity into reduced datasets. Independent spatially explicit methods applied to these latter datasets converged in showing that the extraction of information on long- to medium-range geographical trends and structuring from the overall diversity is possible. All analyses returned the picture of a background clinal variation, with regional discontinuities captured by each of the reduced datasets. Several aspects of our results are confirmed on external STR datasets and replicate those of genome-wide SNP typings. High levels of gene flow were inferred within the main continental areas by coalescent simulations. These results are promising from a microevolutionary perspective, in view of the fast pace at which forensic data are being accumulated for many locales. It is foreseeable that this will allow the exploitation of an invaluable genotypic resource, assembled for other (forensic) purposes, to clarify important aspects in the formation of local gene pools.
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Affiliation(s)
| | | | - Nejat Akar
- Pediatrics Department, TOBB-Economy and Technology University Hospital, Ankara, Turkey
| | | | | | - Radim Brdicka
- Institute of Haematology and Blood Transfusion, Praha, Czech Republic
| | - Carla Jodice
- Department of Biology, University "Tor Vergata", Rome, Italy
| | - Andrea Novelletto
- Department of Biology, University "Tor Vergata", Rome, Italy
- * E-mail:
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De Rosa S, Chiefari E, Salerno N, Ventura V, D'Ascoli GL, Arcidiacono B, Ambrosio G, Bilotta FL, Torella D, Foti D, Indolfi C, Brunetti A. HMGA1 is a novel candidate gene for myocardial infarction susceptibility. Int J Cardiol 2016; 227:331-334. [PMID: 27839822 DOI: 10.1016/j.ijcard.2016.11.088] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/06/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Acute Myocardial infarction (AMI), a leading cause of morbidity and mortality worldwide, is a dreadful acute complication of coronary atherosclerosis. Type 2 diabetes mellitus (T2DM) is associated with an increased risk of developing AMI. The architectural transcription factor high-mobility-group AT-hook 1 (HMGA1) has been involved in atherosclerosis, plaque formation, inflammation, and in the pathogenesis of insulin resistance and T2DM. An association of the HMGA1 rs146052672 variant with T2DM has been recently reported. Thus, our aim was to evaluate whether this variant was also associated with AMI. METHODS AND RESULTS In a case-control study from Calabria (Southern Italy), we enrolled 254 consecutive, unrelated, patients with first diagnosis of AMI, and 508 age, sex-matched controls. Genotyping of the rs146052672 was performed using the TaqMan allelic discrimination method. We found that this variant was present in 7.9% of AMI patients and in 3.1% of controls (p=0.003). Multiple logistic regression confirmed that the rs146052672 was significantly associated with AMI (OR=2.54; p=0.002), and this association was independent of classical cardiovascular risk factors such as gender, hypertension, obesity and T2DM (for all, p<0.05). CONCLUSIONS Our findings demonstrate that a relationship exists between the HMGA1 rs146052672 variant and AMI, suggesting that defects at the HMGA1 locus may play a pathogenetic role in AMI, in the absence of T2DM and other cardiovascular risk factors.
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Affiliation(s)
- Salvatore De Rosa
- Division of Cardiology, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Eusebio Chiefari
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, 88100 Catanzaro, Italy
| | - Nadia Salerno
- Division of Cardiology, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Valeria Ventura
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, 88100 Catanzaro, Italy
| | - Greta Luana D'Ascoli
- Division of Cardiology, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Biagio Arcidiacono
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, 88100 Catanzaro, Italy
| | - Giuseppe Ambrosio
- Division of Cardiology, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | | | - Daniele Torella
- Division of Cardiology, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Daniela Foti
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, 88100 Catanzaro, Italy
| | - Ciro Indolfi
- Division of Cardiology, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy; URT-CNR, Department of Medicine, Consiglio Nazionale delle Ricerche of IFC, Catanzaro, Italy.
| | - Antonio Brunetti
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, 88100 Catanzaro, Italy.
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Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula. Sci Rep 2016; 6:32513. [PMID: 27582244 PMCID: PMC5007512 DOI: 10.1038/srep32513] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/08/2016] [Indexed: 01/23/2023] Open
Abstract
The Italian peninsula has long represented a natural hub for human migrations across
the Mediterranean area, being involved in several prehistoric and historical
population movements. Coupled with a patchy environmental landscape entailing
different ecological/cultural selective pressures, this might have produced peculiar
patterns of population structure and local adaptations responsible for heterogeneous
genomic background of present-day Italians. To disentangle this complex scenario,
genome-wide data from 780 Italian individuals were generated and set into the
context of European/Mediterranean genomic diversity by comparison with genotypes
from 50 populations. To maximize possibility of pinpointing functional genomic
regions that have played adaptive roles during Italian natural history, our survey
included also ~250,000 exomic markers and ~20,000
coding/regulatory variants with well-established clinical relevance. This enabled
fine-grained dissection of Italian population structure through the identification
of clusters of genetically homogeneous provinces and of genomic regions underlying
their local adaptations. Description of such patterns disclosed crucial implications
for understanding differential susceptibility to some inflammatory/autoimmune
disorders, coronary artery disease and type 2 diabetes of diverse Italian
subpopulations, suggesting the evolutionary causes that made some of them
particularly exposed to the metabolic and immune challenges imposed by dietary and
lifestyle shifts that involved western societies in the last centuries.
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Testa A, Prudente S, Leonardis D, Spoto B, Sanguedolce MC, Parlongo RM, Tripepi G, Rizza S, Mallamaci F, Federici M, Trischitta V, Zoccali C. A genetic marker of hyperuricemia predicts cardiovascular events in a meta-analysis of three cohort studies in high risk patients. Nutr Metab Cardiovasc Dis 2015; 25:1087-1094. [PMID: 26607700 DOI: 10.1016/j.numecd.2015.08.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/24/2015] [Accepted: 08/12/2015] [Indexed: 01/05/2023]
Abstract
INTRODUCTION The strongest genetic marker of uric acid levels, the rs734553 SNP in the GLUT9 urate transporter gene, predicts progression to kidney failure in CKD patients and associates with systolic BP and carotid intima media thickness in family-based studies. METHODS Since genes are transmitted randomly (Mendelian randomization) we used this gene polymorphism as an unconfounded research instrument to further explore the link between uric acid and cardiovascular disease (cardiovascular death, and non-fatal myocardial infarction and stroke) in a meta-analysis of three cohort studies formed by high risk patients (MAURO: 755 CKD patients; GHS: 353 type 2 diabetics and coronary artery disease and the TVAS: 119 patients with myocardial infarction). RESULTS In separate analyses of the three cohorts, the incidence rate of CV events was higher in patients with the rs734553 risk (T) allele (TT/GT) than in those without (GG patients) and the HR in TT/GT patients in the three cohorts (range 1.72-2.14) coherently signaled an excessive cardiovascular risk with no heterogeneity (I2 = 0.01). The meta-analytical estimate (total number of patients, n = 1227; total CV events, n = 222) of the HR for the combined end-point in TT/GT patients was twice higher (pooled HR: 2.04, 95% CI: 1.11-3.75, P = 0.02) than in GG homozygotes. CONCLUSIONS The T allele of the rs734553 polymorphism in the GLUT9 gene predicts a doubling in the risk for incident cardiovascular events in patients at high cardiovascular risk. Findings in this study are compatible with the hypothesis of a causal role of hyperuricemia in cardiovascular disease in high risk conditions.
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Affiliation(s)
- A Testa
- CNR-IFC, Research Unit of Clinical Epidemiology and Physiopathology of Renal Disease and Hypertension, Reggio Calabria, Italy
| | - S Prudente
- IRCCS Casa Sollievo della Sofferenza Mendel Laboratory, San Giovanni Rotondo, Italy
| | - D Leonardis
- CNR-IFC, Research Unit of Clinical Epidemiology and Physiopathology of Renal Disease and Hypertension, Reggio Calabria, Italy
| | - B Spoto
- CNR-IFC, Research Unit of Clinical Epidemiology and Physiopathology of Renal Disease and Hypertension, Reggio Calabria, Italy
| | - M C Sanguedolce
- CNR-IFC, Research Unit of Clinical Epidemiology and Physiopathology of Renal Disease and Hypertension, Reggio Calabria, Italy
| | - R M Parlongo
- CNR-IFC, Research Unit of Clinical Epidemiology and Physiopathology of Renal Disease and Hypertension, Reggio Calabria, Italy
| | - G Tripepi
- CNR-IFC, Research Unit of Clinical Epidemiology and Physiopathology of Renal Disease and Hypertension, Reggio Calabria, Italy
| | - S Rizza
- Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - F Mallamaci
- CNR-IFC, Research Unit of Clinical Epidemiology and Physiopathology of Renal Disease and Hypertension, Reggio Calabria, Italy
| | - M Federici
- Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - V Trischitta
- IRCCS Casa Sollievo della Sofferenza Mendel Laboratory, San Giovanni Rotondo, Italy; Research Unit of Diabetes and Endocrine Diseases IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - C Zoccali
- CNR-IFC, Research Unit of Clinical Epidemiology and Physiopathology of Renal Disease and Hypertension, Reggio Calabria, Italy.
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Fiorito G, Di Gaetano C, Guarrera S, Rosa F, Feldman MW, Piazza A, Matullo G. The Italian genome reflects the history of Europe and the Mediterranean basin. Eur J Hum Genet 2015; 24:1056-62. [PMID: 26554880 DOI: 10.1038/ejhg.2015.233] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 11/09/2022] Open
Abstract
Recent scientific literature has highlighted the relevance of population genetic studies both for disease association mapping in admixed populations and for understanding the history of human migrations. Deeper insight into the history of the Italian population is critical for understanding the peopling of Europe. Because of its crucial position at the centre of the Mediterranean basin, the Italian peninsula has experienced a complex history of colonization and migration whose genetic signatures are still present in contemporary Italians. In this study, we investigated genomic variation in the Italian population using 2.5 million single-nucleotide polymorphisms in a sample of more than 300 unrelated Italian subjects with well-defined geographical origins. We combined several analytical approaches to interpret genome-wide data on 1272 individuals from European, Middle Eastern, and North African populations. We detected three major ancestral components contributing different proportions across the Italian peninsula, and signatures of continuous gene flow within Italy, which have produced remarkable genetic variability among contemporary Italians. In addition, we have extracted novel details about the Italian population's ancestry, identifying the genetic signatures of major historical events in Europe and the Mediterranean basin from the Neolithic (e.g., peopling of Sardinia) to recent times (e.g., 'barbarian invasion' of Northern and Central Italy). These results are valuable for further genetic, epidemiological and forensic studies in Italy and in Europe.
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Affiliation(s)
- Giovanni Fiorito
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Cornelia Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Simonetta Guarrera
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Fabio Rosa
- HuGeF Human Genetics Foundation, Turin, Italy
| | | | - Alberto Piazza
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
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Parolo S, Lisa A, Gentilini D, Di Blasio AM, Barlera S, Nicolis EB, Boncoraglio GB, Parati EA, Bione S. Characterization of the biological processes shaping the genetic structure of the Italian population. BMC Genet 2015; 16:132. [PMID: 26553317 PMCID: PMC4640365 DOI: 10.1186/s12863-015-0293-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/03/2015] [Indexed: 12/11/2022] Open
Abstract
Background The genetic structure of human populations is the outcome of the combined action of different processes such as demographic dynamics and natural selection. Several efforts toward the characterization of population genetic architectures and the identification of adaptation signatures were recently made. In this study, we provide a genome-wide depiction of the Italian population structure and the analysis of the major determinants of the current existing genetic variation. Results We defined and characterized 210 genomic loci associated with the first Principal Component calculated on the Italian genotypic data and correlated to the North–south genetic gradient. Using a gene-enrichment approach we identified the immune function as primarily involved in the Italian population differentiation and we described a locus on chromosome 13 showing combined evidence of North–south diversification in allele frequencies and signs of recent positive selection. In this region our bioinformatics analysis pinpointed an uncharacterized long intergenic non-coding (lincRNA), whose expression appeared specific for immune-related tissues suggesting its relevance for the immune function. Conclusions Our study, combining population genetic analyses with biological insights provides a description of the Italian genetic structure that in future could contribute to the evaluation of complex diseases risk in the population context. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0293-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Parolo
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
| | - Antonella Lisa
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
| | - Davide Gentilini
- Molecular Biology Laboratory, Istituto Auxologico Italiano, Milan, Italy.
| | | | - Simona Barlera
- Department of Cardiovascular Research, IRCCS Mario Negri Institute for Pharmacological Research, Milan, Italy.
| | - Enrico B Nicolis
- Department of Cardiovascular Research, IRCCS Mario Negri Institute for Pharmacological Research, Milan, Italy.
| | - Giorgio B Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Eugenio A Parati
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Silvia Bione
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
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Chiefari E, Capula C, Vero A, Oliverio R, Puccio L, Liguori R, Pullano V, Greco M, Foti D, Tirinato D, Vero R, Brunetti A. Add-On Treatment with Liraglutide Improves Glycemic Control in Patients with Type 2 Diabetes on Metformin Therapy. Diabetes Technol Ther 2015; 17:468-74. [PMID: 25844858 DOI: 10.1089/dia.2014.0412] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Liraglutide is a glucagon-like peptide-1 receptor analog recently approved for the treatment of type 2 diabetes mellitus (T2DM). We aimed to assess the efficacy and safety of liraglutide versus glimepiride, as adjunct treatments to metformin, in achieving glycemic control in Italian patients with T2DM uncontrolled by metformin alone. SUBJECTS AND METHODS One hundred seventy-nine diabetes patients treated with metformin plus liraglutide (1.8 mg) or glimepiride (4 mg) were retrospectively assessed at baseline, during, and after 18 months of continuous therapy. RESULTS Treatment with liraglutide resulted in mean decreases in hemoglobin A1c (HbA1c) of -1.4%, when compared with glimepiride (-0.4%) (P < 0.001), and was followed by a significant reduction (P < 0.001) in fasting plasma glucose. Variations in HbA1c occurred independently from weight loss, which was significantly reduced (P < 0.001) in liraglutide-treated patients. The percentage of subjects reaching HbA1c levels below 7% or ≤ 6.5% was significantly different between the two treated groups (P < 0.001). Treatment with liraglutide reduced waist circumference (WC) (P < 0.001) and decreased both systolic and diastolic blood pressure (BP) (P < 0.001). It is interesting that the study also showed the impact of female gender in predicting a better glycemic response to liraglutide (P = 0.028). CONCLUSIONS Liraglutide was more effective than glimepiride in reducing HbA1c levels in treated patients with T2DM. This was evident in both genders, but particularly in women. Furthermore, liraglutide reduced body weight, WC, and BP, which are critical risk factors for cardiovascular disease.
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Affiliation(s)
- Eusebio Chiefari
- 1 Department of Health Sciences, University "Magna Græcia" of Catanzaro , Catanzaro, Italy
| | - Carmelo Capula
- 2 Complex Operative Structure of Endocrinology-Diabetology, Pugliese-Ciaccio Hospital , Catanzaro, Italy
| | - Ada Vero
- 2 Complex Operative Structure of Endocrinology-Diabetology, Pugliese-Ciaccio Hospital , Catanzaro, Italy
| | - Rosa Oliverio
- 1 Department of Health Sciences, University "Magna Græcia" of Catanzaro , Catanzaro, Italy
| | - Luigi Puccio
- 2 Complex Operative Structure of Endocrinology-Diabetology, Pugliese-Ciaccio Hospital , Catanzaro, Italy
| | - Rossella Liguori
- 1 Department of Health Sciences, University "Magna Græcia" of Catanzaro , Catanzaro, Italy
| | - Vittorio Pullano
- 2 Complex Operative Structure of Endocrinology-Diabetology, Pugliese-Ciaccio Hospital , Catanzaro, Italy
| | - Manfredi Greco
- 3 Department of Experimental and Clinical Medicine, University "Magna Græcia" of Catanzaro , Catanzaro, Italy
| | - Daniela Foti
- 1 Department of Health Sciences, University "Magna Græcia" of Catanzaro , Catanzaro, Italy
| | | | - Raffaella Vero
- 2 Complex Operative Structure of Endocrinology-Diabetology, Pugliese-Ciaccio Hospital , Catanzaro, Italy
| | - Antonio Brunetti
- 1 Department of Health Sciences, University "Magna Græcia" of Catanzaro , Catanzaro, Italy
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A polymorphism in the major gene regulating serum uric acid associates with clinic SBP and the white-coat effect in a family-based study. J Hypertens 2015; 32:1621-8; discussion 1628. [PMID: 24805955 DOI: 10.1097/hjh.0000000000000224] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Hyperuricemia associates with hypertension, but it is uncertain whether this relationship is causal in nature. Glucose transporter 9 (GLUT9) gene is a major genetic determinant of plasma uric acid levels in humans. Since polymorphisms are randomly distributed at mating (Mendelian randomization), studies based on GLUT9 polymorphisms may provide unconfounded assessment of the nature of the link between uric acid and hypertension. METHODS We tested the association between uric acid, the rs734553 polymorphism of the GLUT9 gene and arterial pressure in a family-based study including 449 individuals in a genetically homogenous population in Southern Italy. RESULTS Serum uric acid levels were strongly associated (P < 0.001) with all components of clinic and 24-h ambulatory blood pressures (BPs). However, only clinic SBP and the white-coat effect (the difference in clinic systolic and daytime systolic ambulatory blood pressure monitoring) associations remained significant after adjustment for classical risk factor and the estimated glomerular filtration rate. Serum uric acid was strongly associated with the risk allele (T) of the rs734553 polymorphism (P < 0.001). Furthermore, TT individuals showed higher clinic SBP (129 + SEM 1 mmHg) than GT (125 + 1 mmHg) and GG individuals (122 + 3 mmHg), as well as a higher white-coat effect (P = 0.02), confirming that the association between uric acid and these BP components is unconfounded by environmental risk factors. CONCLUSION Results in this family-based study are compatible with the hypothesis that uric acid is a causal risk factor for hypertension. Trials testing uric acid-lowering interventions are needed to definitively establish the causal implication of hyperuricemia in human hypertension. [Corrected]
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Unravelling the hidden ancestry of American admixed populations. Nat Commun 2015; 6:6596. [PMID: 25803618 PMCID: PMC4374169 DOI: 10.1038/ncomms7596] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/10/2015] [Indexed: 12/16/2022] Open
Abstract
The movement of people into the Americas has brought different populations into contact, and contemporary American genomes are the product of a range of complex admixture events. Here we apply a haplotype-based ancestry identification approach to a large set of genome-wide SNP data from a variety of American, European and African populations to determine the contributions of different ancestral populations to the Americas. Our results provide a fine-scale characterization of the source populations, identify a series of novel, previously unreported contributions from Africa and Europe and highlight geohistorical structure in the ancestry of American admixed populations.
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A polymorphism at the translation start site of the vitamin D receptor gene is associated with the response to anti-osteoporotic therapy in postmenopausal women from southern Italy. Int J Mol Sci 2015; 16:5452-66. [PMID: 25764158 PMCID: PMC4394486 DOI: 10.3390/ijms16035452] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/17/2015] [Accepted: 03/04/2015] [Indexed: 11/24/2022] Open
Abstract
The present study investigated the effect of two single nucleotide polymorphisms (SNPs) of the vitamin D receptor (VDR) gene, rs1544410 A/G and rs2228570 C/T, in modulating bone mineral density (BMD) and the response to treatment with bisphosphonates or strontium ranelate in postmenopausal osteoporosis (PMO). Four hundred eighteen postmenopausal women from Southern Italy treated with bisphosphonates or strontium ranelate for three years were enrolled and stratified according to their genotype. Changes in BMD were expressed as the delta t-score (Δt-score). Allelic frequencies for rs1544410 A/GSNP were 11.2% AA, 50.0% GA and 38.8% GG; for rs2228570 C/TSNP were 54.8% CC, 39.5% TC and 5.7% TT. TT carriers showed a lower t-score than TC and CC (both p < 0.02) genotypes and were more responsive to the therapy when compared to both TC (p < 0.02) and CC (p < 0.05) carriers. Specifically, TT carriers receiving alendronate demonstrated a significant improvement of the Δt-score compared to TC and CC (both p < 0.0001) carriers. After adjustment for confounders, the Δt-score showed evidence of a statistically significant positive association with TT in all treatments considered. Therapy response was independent of rs1544410 A/G SNP; instead, rs2228570 C/TSNP was associated with a better response to antiresorptive treatment, thus suggesting that the therapy for PMO should be personalized.
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Mallamaci F, Testa A, Leonardis D, Tripepi R, Pisano A, Spoto B, Sanguedolce MC, Parlongo RM, Tripepi G, Zoccali C. A Genetic Marker of Uric Acid Level, Carotid Atherosclerosis, and Arterial Stiffness: A Family-Based Study. Am J Kidney Dis 2015; 65:294-302. [DOI: 10.1053/j.ajkd.2014.07.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/28/2014] [Indexed: 11/11/2022]
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Spoto B, Mattace-Raso F, Sijbrands E, Leonardis D, Testa A, Pisano A, Pizzini P, Cutrupi S, Parlongo RM, D'Arrigo G, Tripepi G, Mallamaci F, Zoccali C. Association of IL-6 and a functional polymorphism in the IL-6 gene with cardiovascular events in patients with CKD. Clin J Am Soc Nephrol 2014; 10:232-40. [PMID: 25492254 DOI: 10.2215/cjn.07000714] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVES High serum IL-6 is a major risk factor for cardiovascular disease (CVD) in the general population. This cytokine is substantially increased in patients with CKD, but it is still unknown whether the link between IL-6 and CVD in CKD is causal in nature. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS In a cohort of 755 patients with stages 2-5 CKD, consecutively recruited from 22 nephrology units in southern Italy, this study assessed the relationship of serum IL-6 with history of CVD, as well as with incident cardiovascular (CV) events (mean follow up±SD, 31±10 months) and used the functional polymorphism (-174 G/C) in the promoter of the IL-6 gene to investigate whether the link between IL-6 and CV events is causal. RESULTS In adjusted analyses, serum IL-6 above the median value was associated with history of CVD (P<0.001) and predicted the incidence rate of CV events (hazard ratio, 1.66; 95% confidence interval [95% CI], 1.11 to 2.49; P=0.01). Patients homozygous for the risk allele (C) of the -174 G/C polymorphism had higher levels of IL-6 than did those with other genotypes (P=0.04). Homozygous CC patients more frequently had a history of CVD (odds ratio, 2.15; 95% CI, 1.15 to 4.00; P=0.02) as well as a 87% higher rate of incident CV events (hazard ratio, 1.87; 95% CI, 1.02 to 3.44; P=0.04) compared with other genotypes. CONCLUSIONS In patients with stages 2-5 CKD, high serum IL-6 is associated with history of CVD and predicts incident CV events. The parallel relationship with history of CVD and incident CV events of the -174 G/C polymorphism in the IL-6 gene suggests that IL-6 may be causally involved in the high CV risk in this population.
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Affiliation(s)
- Belinda Spoto
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
| | - Francesco Mattace-Raso
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Eric Sijbrands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Daniela Leonardis
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
| | - Alessandra Testa
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
| | - Anna Pisano
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
| | - Patrizia Pizzini
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
| | - Sebastiano Cutrupi
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
| | - Rosa M Parlongo
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
| | - Graziella D'Arrigo
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
| | - Giovanni Tripepi
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
| | - Francesca Mallamaci
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
| | - Carmine Zoccali
- National Research Council of Italy-Institute of Clinical Physiology & Institute of Biomedicine and Molecular Immunology & Nephrology, Dialysis and Transplantation Unit of Reggio, Calabria, Italy; and
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Fine-scale human genetic structure in Western France. Eur J Hum Genet 2014; 23:831-6. [PMID: 25182131 DOI: 10.1038/ejhg.2014.175] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 07/21/2014] [Accepted: 07/30/2014] [Indexed: 11/08/2022] Open
Abstract
The difficulties arising from association analysis with rare variants underline the importance of suitable reference population cohorts, which integrate detailed spatial information. We analyzed a sample of 1684 individuals from Western France, who were genotyped at genome-wide level, from two cohorts D.E.S.I.R and CavsGen. We found that fine-scale population structure occurs at the scale of Western France, with distinct admixture proportions for individuals originating from the Brittany Region and the Vendée Department. Genetic differentiation increases with distance at a high rate in these two parts of Northwestern France and linkage disequilibrium is higher in Brittany suggesting a lower effective population size. When looking for genomic regions informative about Breton origin, we found two prominent associated regions that include the lactase region and the HLA complex. For both the lactase and the HLA regions, there is a low differentiation between Bretons and Irish, and this is also found at the genome-wide level. At a more refined scale, and within the Pays de la Loire Region, we also found evidence of fine-scale population structure, although principal component analysis showed that individuals from different departments cannot be confidently discriminated. Because of the evidence for fine-scale genetic structure in Western France, we anticipate that rare and geographically localized variants will be identified in future full-sequence analyses.
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Capula C, Chiefari E, Vero A, Foti DP, Brunetti A, Vero R. Prevalence and predictors of postpartum glucose intolerance in Italian women with gestational diabetes mellitus. Diabetes Res Clin Pract 2014; 105:223-30. [PMID: 24931701 DOI: 10.1016/j.diabres.2014.05.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 04/25/2014] [Accepted: 05/18/2014] [Indexed: 02/07/2023]
Abstract
AIMS To determine the prevalence of both prediabetes and type 2 diabetes mellitus (T2DM) by postpartum oral glucose tolerance test (ppOGTT) in Italian women diagnosed with gestational diabetes mellitus (GDM), and identify antepartum predictors of glucose intolerance. METHODS Retrospective study of 454 Caucasian women that underwent a 75g OGTT between 6 and 12 weeks postpartum in Calabria (Southern Italy) between 2004 and 2012. Prediabetes and T2DM were diagnosed according to the American Diabetes Association (ADA) criteria. Data were examined by univariate analysis and multiple regression analysis. RESULTS 290 women (63.9%) were normal, 146 (32.1%) had prediabetes (85 impaired fasting glycemia; 61 impaired glucose tolerance), and 18 (4.0%) had T2DM. Of the continuous variables, pre-pregnancy body mass index (BMI), age at pregnancy, fasting plasma glucose (FPG) at gravid OGTT, and week at diagnosis of GDM were associated with prediabetes and T2DM, whereas the parity was associated with T2DM only. For categorical traits, pre-pregnancy BMI ≥ 25 and previous diagnosis of polycystic ovary syndrome (PCOS) emerged as the strongest predictors of prediabetes whereas the strongest predictors of T2DM were FPG ≥ 100 mg/dl (5.6 mmol/l) at GDM diagnosis and pre-pregnancy BMI ≥ 25. Moreover, FPG at GDM screening was a good predictor of T2DM after receiver-operating-characteristic analysis. CONCLUSIONS Our findings confirm the high prevalence of glucose intolerance in the early postpartum period in women with previous GDM. PCOS emerges as a new strong antepartum predictor of prediabetes.
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Affiliation(s)
- Carmelo Capula
- Complex Operative Structure of Endocrinology-Diabetology, Pugliese-Ciaccio Hospital, 88100 Catanzaro, Italy
| | - Eusebio Chiefari
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, 88100 Catanzaro, Italy
| | - Anna Vero
- Complex Operative Structure of Endocrinology-Diabetology, Pugliese-Ciaccio Hospital, 88100 Catanzaro, Italy
| | - Daniela P Foti
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, 88100 Catanzaro, Italy
| | - Antonio Brunetti
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, 88100 Catanzaro, Italy.
| | - Raffaella Vero
- Complex Operative Structure of Endocrinology-Diabetology, Pugliese-Ciaccio Hospital, 88100 Catanzaro, Italy
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An ancient Mediterranean melting pot: investigating the uniparental genetic structure and population history of sicily and southern Italy. PLoS One 2014; 9:e96074. [PMID: 24788788 PMCID: PMC4005757 DOI: 10.1371/journal.pone.0096074] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/03/2014] [Indexed: 11/19/2022] Open
Abstract
Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.
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A polymorphism of HMGA1 is associated with increased risk of metabolic syndrome and related components. Sci Rep 2014; 3:1491. [PMID: 23512162 PMCID: PMC3603272 DOI: 10.1038/srep01491] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 03/04/2013] [Indexed: 12/11/2022] Open
Abstract
The metabolic syndrome (MetS) is a common disorder, where systemic insulin-resistance is associated with increased risk for type 2 diabetes (T2D) and cardiovascular disease. Identifying genetic traits influencing risk and progression of MetS is important. We and others previously reported a functional HMGA1 gene variant, rs146052672, predisposing to T2D. Here we investigated the association of rs146052672 variant with MetS and related components. In a case-control study from Italy and Turkey, increased risk of MetS was seen among carriers of the HMGA1 variant. In the larger Italian cohort, this variant positively correlated with BMI, hyperglycemia and insulin-resistance, and negatively correlated with serum HDL-cholesterol. Association between rs146052672 variant and MetS occurred independently of T2D, indicating that HMGA1 gene defects play a pathogenetic role in MetS and other insulin-resistance-related conditions. Overall, our results indicate that the rs146052672 variant represents an early predictive marker of MetS, as well as a predictive tool for therapy.
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Sardinians genetic background explained by runs of homozygosity and genomic regions under positive selection. PLoS One 2014; 9:e91237. [PMID: 24651212 PMCID: PMC3961211 DOI: 10.1371/journal.pone.0091237] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 02/10/2014] [Indexed: 11/19/2022] Open
Abstract
The peculiar position of Sardinia in the Mediterranean sea has rendered its population an interesting biogeographical isolate. The aim of this study was to investigate the genetic population structure, as well as to estimate Runs of Homozygosity and regions under positive selection, using about 1.2 million single nucleotide polymorphisms genotyped in 1077 Sardinian individuals. Using four different methods--fixation index, inflation factor, principal component analysis and ancestry estimation--we were able to highlight, as expected for a genetic isolate, the high internal homogeneity of the island. Sardinians showed a higher percentage of genome covered by RoHs>0.5 Mb (F(RoH%0.5)) when compared to peninsular Italians, with the only exception of the area surrounding Alghero. We furthermore identified 9 genomic regions showing signs of positive selection and, we re-captured many previously inferred signals. Other regions harbor novel candidate genes for positive selection, like TMEM252, or regions containing long non coding RNA. With the present study we confirmed the high genetic homogeneity of Sardinia that may be explained by the shared ancestry combined with the action of evolutionary forces.
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Gazave E, Ma L, Chang D, Coventry A, Gao F, Muzny D, Boerwinkle E, Gibbs RA, Sing CF, Clark AG, Keinan A. Neutral genomic regions refine models of recent rapid human population growth. Proc Natl Acad Sci U S A 2014; 111:757-62. [PMID: 24379384 PMCID: PMC3896169 DOI: 10.1073/pnas.1310398110] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human populations have experienced dramatic growth since the Neolithic revolution. Recent studies that sequenced a very large number of individuals observed an extreme excess of rare variants and provided clear evidence of recent rapid growth in effective population size, although estimates have varied greatly among studies. All these studies were based on protein-coding genes, in which variants are also impacted by natural selection. In this study, we introduce targeted sequencing data for studying recent human history with minimal confounding by natural selection. We sequenced loci far from genes that meet a wide array of additional criteria such that mutations in these loci are putatively neutral. As population structure also skews allele frequencies, we sequenced 500 individuals of relatively homogeneous ancestry by first analyzing the population structure of 9,716 European Americans. We used very high coverage sequencing to reliably call rare variants and fit an extensive array of models of recent European demographic history to the site frequency spectrum. The best-fit model estimates ∼ 3.4% growth per generation during the last ∼ 140 generations, resulting in a population size increase of two orders of magnitude. This model fits the data very well, largely due to our observation that assumptions of more ancient demography can impact estimates of recent growth. This observation and results also shed light on the discrepancy in demographic estimates among recent studies.
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Affiliation(s)
- Elodie Gazave
- Departments of Biological Statistics and Computational Biology and
| | - Li Ma
- Departments of Biological Statistics and Computational Biology and
| | - Diana Chang
- Departments of Biological Statistics and Computational Biology and
| | - Alex Coventry
- Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Feng Gao
- Departments of Biological Statistics and Computational Biology and
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; and
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; and
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030; and
| | - Charles F. Sing
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48105
| | - Andrew G. Clark
- Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Alon Keinan
- Departments of Biological Statistics and Computational Biology and
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Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P, Yang-Yao D, Manry J, Ciani G, Luiselli D, Quintana-Murci L, Comas D, Pettener D. Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata. PLoS One 2013; 8:e65441. [PMID: 23734255 PMCID: PMC3666984 DOI: 10.1371/journal.pone.0065441] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/24/2013] [Indexed: 11/18/2022] Open
Abstract
Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ∼900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West–South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe.
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Affiliation(s)
- Alessio Boattini
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Begoña Martinez-Cruz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Stefania Sarno
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Christine Harmant
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - Antonella Useli
- Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy
| | - Paula Sanz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniele Yang-Yao
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Jeremy Manry
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - Graziella Ciani
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Donata Luiselli
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Lluis Quintana-Murci
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail: (DC); (DP)
| | - Davide Pettener
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- * E-mail: (DC); (DP)
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Coubard OA. A method for processing multivariate data in medical studies. Stat Med 2013; 32:3436-48. [PMID: 23553725 DOI: 10.1002/sim.5788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 01/12/2013] [Accepted: 01/30/2013] [Indexed: 11/09/2022]
Abstract
Traditional displays of principal component analyses lack readability to discriminate between putative clusters of variables or cases. Here, the author proposes a method that clusterizes and visualizes variables or cases through principal component analyses thus facilitating their analysis. The method displays pre-determined clusters of variables or cases as urchins that each has a soma (the average point) and spines (the individual variables or cases). Through three examples in the field of neuropsychology, the author illustrates how urchins help examine the modularity of cognitive tasks on the one hand and identify groups of healthy versus brain-damaged participants on the other hand. Some of the data used in this article were obtained from the Alzheimer's Disease Neuroimaging Initiative database. The urchin method was implemented in MATLAB, and the source code is available in the Supporting information. Urchins can be useful in biomedical studies to identify distinct phenomena at first glance, each having several measures (clusters of variables) or distinct groups of participants (clusters of cases).
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Affiliation(s)
- Olivier A Coubard
- The Neuropsychological Laboratory, CNS-Fed, 39 rue Meaux, 75019 Paris, France.
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