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Justicia-Grande AJ, Gómez-Ríal J, Rivero-Calle I, Pischedda S, Curras-Tuala MJ, Gómez-Carballa A, Cebey-López M, Pardo-Seco J, Méndez-Gallart R, Fernández-Seara MJ, Salas A, Martinón-Torres F. Case Report: Two Monochorionic Twins With a Critically Different Course of Progressive Osseus Heteroplasia. Front Pediatr 2021; 9:662669. [PMID: 34249809 PMCID: PMC8260848 DOI: 10.3389/fped.2021.662669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Progressive osseous heteroplasia (POH; OMIM 166350) is a rare autosomal-dominant genetic disorder in which extra-skeletal bone forms within skin and muscle tissue. POH is one of the clinical manifestations of an inactivating mutation in the GNAS gene. GNAS gene alterations are difficult matter to address, as GNAS alleles show genetic imprinting and produce several transcript products, and the same mutation may lead to strikingly different phenotypes. Also, most of the publications concerning POH patients are either clinical depictions of a case (or a case series), descriptions of their genetic background, or a tentative correlation of both clinical and molecular findings. Treatment for POH is rarely addressed, and POH still lacks therapeutic options. We describe a unique case of POH in two monochorionic twins, who presented an almost asymptomatic vs. the severe clinical course, despite sharing the same mutation and genetic background. We also report the results of the therapeutic interventions currently available for heterotopic ossification in the patient with the severe course. This article not only critically supports the assumption that the POH course is strongly influenced by factors beyond genetic background but also remarks the lack of options for patients suffering an orphan disease, even after testing drugs with promising in vitro results.
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Affiliation(s)
- Antonio José Justicia-Grande
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain.,Physical Medicine and Rehabilitation Department, Hospital Clínico Universitario de Santiago de Compostela, A Coruña, Spain
| | - Jose Gómez-Ríal
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain.,Immunology Laboratory, Clinical Laboratory, Hospital Clínico Universitario Santiago de Compostela, A Coruña, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, A Coruña, Spain
| | - Sara Pischedda
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - María José Curras-Tuala
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alberto Gómez-Carballa
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Miriam Cebey-López
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jacobo Pardo-Seco
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Roberto Méndez-Gallart
- Pediatric Surgery, Hospital Clínico Universitario de Santiago de Compostela, A Coruña, Spain
| | - María José Fernández-Seara
- Immunology Laboratory, Clinical Laboratory, Hospital Clínico Universitario Santiago de Compostela, A Coruña, Spain
| | - Antonio Salas
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain.,Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago de Compostela, A Coruña, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, A Coruña, Spain
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2
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Biogeographical origin and timing of the founder ichthyosis TGM1 c.1187G > A mutation in an isolated Ecuadorian population. Sci Rep 2019; 9:7175. [PMID: 31073126 PMCID: PMC6509209 DOI: 10.1038/s41598-019-43133-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 04/11/2019] [Indexed: 11/22/2022] Open
Abstract
An unusually high frequency of the lamellar ichthyosis TGM1 mutation, c.1187G > A, has been observed in the Ecuadorian province of Manabí. Recently, the same mutation has been detected in a Galician patient (Northwest of Spain). By analyzing patterns of genetic variation around this mutation in Ecuadorian patients and population matched controls, we were able to estimate the age of c.1187G > A and the time to their most recent common ancestor (TMRCA) of c.1187G > A Ecuadorian carriers. While the estimated mutation age is 41 generations ago (~1,025 years ago [ya]), the TMRCA of Ecuadorian c.1187G > A carrier haplotypes dates to just 17 generations (~425 ya). Probabilistic-based inferences of local ancestry allowed us to infer a most likely European origin of a few (16% to 30%) Ecuadorian haplotypes carrying this mutation. In addition, inferences on demographic historical changes based on c.1187G > A Ecuadorian carrier haplotypes estimated an exponential population growth starting ~20 generations, compatible with a recent founder effect occurring in Manabí. Two main hypotheses can be considered for the origin of c.1187G > A: (i) the mutation could have arisen in Spain >1,000 ya (being Galicia the possible homeland) and then carried to Ecuador by Spaniards in colonial times ~400 ya, and (ii) two independent mutational events originated this mutation in Ecuador and Galicia. The geographic and cultural characteristics of Manabí could have favored a founder effect that explains the high prevalence of TGM1 c.1187G > A in this region.
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3
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Choudhury A, Aron S, Sengupta D, Hazelhurst S, Ramsay M. African genetic diversity provides novel insights into evolutionary history and local adaptations. Hum Mol Genet 2018; 27:R209-R218. [PMID: 29741686 PMCID: PMC6061870 DOI: 10.1093/hmg/ddy161] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 12/22/2022] Open
Abstract
Genetic variation and susceptibility to disease are shaped by human demographic history and adaptation. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunter-gatherer populations in southern and central Africa; Nilo-Saharan speakers from north and northeast Africa; Afro-Asiatic speakers from north and east Africa; and Niger-Congo speakers who are the predominant ethnolinguistic group spread across most of sub-Saharan Africa. The enormous ethnolinguistic diversity in sub-Saharan African populations is largely paralleled by extensive genetic diversity and until a decade ago, little was known about detailed origins and divergence of these groups. Results from large-scale population genetic studies, and more recently whole genome sequence data, are unravelling the critical role of events like migration and admixture and environmental factors including diet, infectious diseases and climatic conditions in shaping current population diversity. It is now possible to start providing quantitative estimates of divergence times, population size and dynamic processes that have affected populations and their genetic risk for disease. Finally, the availability of ancient genomes from Africa provides historical insights of unprecedented depth. In this review, we highlight some key interpretations that have emerged from recent African genome studies.
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Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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4
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A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms. Sci Rep 2018; 8:8043. [PMID: 29795312 PMCID: PMC5966427 DOI: 10.1038/s41598-018-26239-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/08/2018] [Indexed: 02/03/2023] Open
Abstract
Recently, a biomarker signature consisting of 2-transcript host RNAs was proposed for discriminating bacterial from viral infections in febrile children. We evaluated the performance of this signature in a different disease scenario, namely a cohort of Mexican children (n = 174) suffering from acute diarrhea of different infectious etiologies. We first examined the admixed background of the patients, indicating that most of them have a predominantly Native American genetic ancestry with a variable amount of European background (ranging from 0% to 57%). The results confirm that the RNA test can discriminate between viral and bacterial causes of infection (t-test; P-value = 6.94×10−11; AUC = 80%; sensitivity: 68% [95% CI: 55%–79%]; specificity: 84% [95% CI: 78%–90%]), but the strength of the signal differs substantially depending on the causal pathogen, with the stronger signal being that of Shigella (P-value = 3.14 × 10−12; AUC = 89; sensitivity: 70% [95% CI: 57%–83%]; specificity: 100% [95% CI: 100%–100%]). The accuracy of this test improves significantly when excluding mild cases (P-value = 2.13 × 10−6; AUC = 85%; sensitivity: 79% [95% CI: 58%–95%]; specificity: 78% [95% CI: 65%–88%]). The results broaden the scope of previous studies by incorporating different pathogens, variable levels of disease severity, and different ancestral background of patients, and add confirmatory support to the clinical utility of these 2-transcript biomarkers.
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5
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Gómez-Carballa A, Pardo-Seco J, Brandini S, Achilli A, Perego UA, Coble MD, Diegoli TM, Álvarez-Iglesias V, Martinón-Torres F, Olivieri A, Torroni A, Salas A. The peopling of South America and the trans-Andean gene flow of the first settlers. Genome Res 2018; 28:767-779. [PMID: 29735605 PMCID: PMC5991523 DOI: 10.1101/gr.234674.118] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/27/2018] [Indexed: 11/25/2022]
Abstract
Genetic and archaeological data indicate that the initial Paleoindian settlers of South America followed two entry routes separated by the Andes and the Amazon rainforest. The interactions between these paths and their impact on the peopling of South America remain unclear. Analysis of genetic variation in the Peruvian Andes and regions located south of the Amazon River might provide clues on this issue. We analyzed mitochondrial DNA variation at different Andean locations and >360,000 autosomal SNPs from 28 Native American ethnic groups to evaluate different trans-Andean demographic scenarios. Our data reveal that the Peruvian Altiplano was an important enclave for early Paleoindian expansions and point to a genetic continuity in the Andes until recent times, which was only marginally affected by gene flow from the Amazonian lowlands. Genomic variation shows a good fit with the archaeological evidence, indicating that the genetic interactions between the descendants of the settlers that followed the Pacific and Atlantic routes were extremely limited.
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Affiliation(s)
- Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, 15706 Galicia, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, 15706 Galicia, Spain
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Ugo A Perego
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Michael D Coble
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Toni M Diegoli
- Office of the Chief Scientist, Defense Forensic Science Center, Ft. Gillem, Georgia 30297, USA.,Analytical Services, Incorporated, Arlington, Virginia 22201, USA
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela, 15706 Galicia, Spain
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27110 Pavia, Italy
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706 Galicia, Spain
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6
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Fortes-Lima C, Gessain A, Ruiz-Linares A, Bortolini MC, Migot-Nabias F, Bellis G, Moreno-Mayar JV, Restrepo BN, Rojas W, Avendaño-Tamayo E, Bedoya G, Orlando L, Salas A, Helgason A, Gilbert MTP, Sikora M, Schroeder H, Dugoujon JM. Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname. Am J Hum Genet 2017; 101:725-736. [PMID: 29100086 DOI: 10.1016/j.ajhg.2017.09.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/22/2017] [Indexed: 01/30/2023] Open
Abstract
The transatlantic slave trade was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of African-descendant Marron populations, we generated genome-wide data (4.3 million markers) from 107 individuals from three African-descendant populations in South America, as well as 124 individuals from six west African populations. Throughout the Americas, thousands of enslaved Africans managed to escape captivity and establish lasting communities, such as the Noir Marron. We find that this population has the highest proportion of African ancestry (∼98%) of any African-descendant population analyzed to date, presumably because of centuries of genetic isolation. By contrast, African-descendant populations in Brazil and Colombia harbor substantially more European and Native American ancestry as a result of their complex admixture histories. Using ancestry tract-length analysis, we detect different dates for the European admixture events in the African-Colombian (1749 CE; confidence interval [CI]: 1737-1764) and African-Brazilian (1796 CE; CI: 1789-1804) populations in our dataset, consistent with the historically attested earlier influx of Africans into Colombia. Furthermore, we find evidence for sex-specific admixture patterns, resulting from predominantly European paternal gene flow. Finally, we detect strong genetic links between the African-descendant populations and specific source populations in Africa on the basis of haplotype sharing patterns. Although the Noir Marron and African-Colombians show stronger affinities with African populations from the Bight of Benin and the Gold Coast, the African-Brazilian population from Rio de Janeiro has greater genetic affinity with Bantu-speaking populations from the Bight of Biafra and west central Africa.
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Affiliation(s)
- Cesar Fortes-Lima
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, AMIS UMR5288, Centre National de la Recherche Scientifique (CNRS) -Université Paul Sabatier Toulouse III, Toulouse 31000, France; Laboratory Eco-Anthropology and Ethno-Biology, UMR7206, CNRS-MNHN-University Paris Diderot, Musée de l'Homme, 17 Place du Trocadéro, 75016 Paris, France
| | - Antoine Gessain
- Oncogenic Virus Epidemiology and Pathophysiology Group, Department of Virology, CNRS UMR3569, Pasteur Institute, Paris 75015, France
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom; Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China; Laboratory of Biocultural Anthropology, Law, Ethics, and Health, CNRS/EFS ADES UMR7268, Aix-Marseille University, Marseille 13824, France
| | - Maria-Cátira Bortolini
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Florence Migot-Nabias
- Mother and Child Facing Tropical Infections (MERIT), Research Institute for Development, Paris 5 University, Sorbonne Paris Cité, Paris 75006, France
| | - Gil Bellis
- French Institute for Demographic Studies, Paris 75020, France
| | - J Víctor Moreno-Mayar
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Berta Nelly Restrepo
- Instituto Colombiano de Medicina Tropical, Universidad CES, Sabaneta, Antioquia 055450, Colombia
| | - Winston Rojas
- Laboratory of Molecular Genetics, Institute of Biology, University of Antioquia, Medellín 050010, Colombia
| | - Efren Avendaño-Tamayo
- Laboratory of Molecular Genetics, Institute of Biology, University of Antioquia, Medellín 050010, Colombia; Grupo de Ciencias Básicas Aplicadas del Tecnológico de Antioquia, Tecnológico de Antioquia - Institución Universitaria, Medellín 050034, Colombia
| | - Gabriel Bedoya
- Laboratory of Molecular Genetics, Institute of Biology, University of Antioquia, Medellín 050010, Colombia
| | - Ludovic Orlando
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, AMIS UMR5288, Centre National de la Recherche Scientifique (CNRS) -Université Paul Sabatier Toulouse III, Toulouse 31000, France; Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain; GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago, Galicia 15782, Spain
| | | | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim 7491, Norway
| | - Martin Sikora
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Hannes Schroeder
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark; Faculty of Archaeology, Leiden University, Leiden 2333, the Netherlands.
| | - Jean-Michel Dugoujon
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, AMIS UMR5288, Centre National de la Recherche Scientifique (CNRS) -Université Paul Sabatier Toulouse III, Toulouse 31000, France.
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7
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Pischedda S, Barral-Arca R, Gómez-Carballa A, Pardo-Seco J, Catelli ML, Álvarez-Iglesias V, Cárdenas JM, Nguyen ND, Ha HH, Le AT, Martinón-Torres F, Vullo C, Salas A. Phylogeographic and genome-wide investigations of Vietnam ethnic groups reveal signatures of complex historical demographic movements. Sci Rep 2017; 7:12630. [PMID: 28974757 PMCID: PMC5626762 DOI: 10.1038/s41598-017-12813-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/14/2017] [Indexed: 01/21/2023] Open
Abstract
The territory of present-day Vietnam was the cradle of one of the world’s earliest civilizations, and one of the first world regions to develop agriculture. We analyzed the mitochondrial DNA (mtDNA) complete control region of six ethnic groups and the mitogenomes from Vietnamese in The 1000 Genomes Project (1000G). Genome-wide data from 1000G (~55k SNPs) were also investigated to explore different demographic scenarios. All Vietnamese carry South East Asian (SEA) haplotypes, which show a moderate geographic and ethnic stratification, with the Mong constituting the most distinctive group. Two new mtDNA clades (M7b1a1f1 and F1f1) point to historical gene flow between the Vietnamese and other neighboring countries. Bayesian-based inferences indicate a time-deep and continuous population growth of Vietnamese, although with some exceptions. The dramatic population decrease experienced by the Cham 700 years ago (ya) fits well with the Nam tiến (“southern expansion”) southwards from their original heartland in the Red River Delta. Autosomal SNPs consistently point to important historical gene flow within mainland SEA, and add support to a main admixture event occurring between Chinese and a southern Asian ancestral composite (mainly represented by the Malay). This admixture event occurred ~800 ya, again coinciding with the Nam tiến.
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Affiliation(s)
- S Pischedda
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - R Barral-Arca
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - A Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - J Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - M L Catelli
- Equipo Argentino de Antropología Forense, Independencia, 644, Córdoba, Argentina
| | - V Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - J M Cárdenas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Grupo de Investigación en Genética Forense - Instituto Nacional de Medicina Legal y Ciencias Forenses, Bogotá, Colombia
| | - N D Nguyen
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - H H Ha
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - A T Le
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - F Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - C Vullo
- Equipo Argentino de Antropología Forense, Independencia, 644, Córdoba, Argentina
| | - A Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain. .,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.
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8
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Copy number alteration of neuropeptides and receptors in multiple cancers. Sci Rep 2017; 7:4598. [PMID: 28676692 PMCID: PMC5496884 DOI: 10.1038/s41598-017-04832-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/22/2017] [Indexed: 11/29/2022] Open
Abstract
Neuropeptides are peptide hormones used as chemical signals by the neuroendocrine system to communicate between cells. Recently, neuropeptides have been recognized for their ability to act as potent cellular growth factors on many cell types, including cancer cells. However, the molecular mechanism for how this occurs is unknown. To clarify the relationship between neuropeptides and cancer, we manually curated a total of 127 human neuropeptide genes by integrating information from the literature, homologous sequences, and database searches. Using human ligand-receptor interaction data, we first identified an interactome of 226 interaction pairs between 93 neuropeptides and 133 G-protein coupled receptors. We further identified four neuropeptide-receptor functional modules with ten or more genes, all of which were highly mutated in multiple cancers. We have identified a number of neuropeptide signaling systems with both oncogenic and tumour-suppressing roles for cancer progression, such as the insulin-like growth factors. By focusing on the neuroendocrine prostate cancer mutational data, we found prevalent amplification of neuropeptide and receptors in about 72% of samples. In summary, we report the first observation of abundant copy number variations on neuropeptides and receptors, which will be valuable for the design of peptide-based cancer prognosis, diagnosis and treatment.
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Pardo-Seco J, Llull C, Berardi G, Gómez A, Andreatta F, Martinón-Torres F, Toscanini U, Salas A. Genomic continuity of Argentinean Mennonites. Sci Rep 2016; 6:36392. [PMID: 27824108 PMCID: PMC5099698 DOI: 10.1038/srep36392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/11/2016] [Indexed: 12/04/2022] Open
Abstract
Mennonites are Anabaptist communities that originated in Central Europe about 500 years ago. They initially migrated to different European countries, and in the early 18th century they established their first communities in North America, from where they moved to other American regions. We aimed to analyze an Argentinean Mennonite congregation from a genome-wide perspective by way of investigating >580.000 autosomal SNPs. Several analyses show that Argentinean Mennonites have European ancestry without signatures of admixture with other non-European American populations. Among the worldwide datasets used for population comparison, the CEU, which is the best-subrogated Central European population existing in The 1000 Genome Project, is the dataset showing the closest genome affinity to the Mennonites. When compared to other European population samples, the Mennonites show higher inbreeding coefficient values. Argentinean Mennonites show signatures of genetic continuity with no evidence of admixture with Americans of Native American or sub-Saharan African ancestry. Their genome indicates the existence of an increased endogamy compared to other Europeans most likely mirroring their lifestyle that involve small communities and historical consanguineous marriages.
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Affiliation(s)
- Jacobo Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
| | - Cintia Llull
- PRICAI-Fundación Favaloro, Buenos Aires, Argentina
| | | | - Andrea Gómez
- PRICAI-Fundación Favaloro, Buenos Aires, Argentina
| | | | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain.,Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | | | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
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