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Serrano JG, Ordóñez AC, Santana J, Sánchez-Cañadillas E, Arnay M, Rodríguez-Rodríguez A, Morales J, Velasco-Vázquez J, Alberto-Barroso V, Delgado-Darias T, de Mercadal MCC, Hernández JC, Moreno-Benítez MA, Pais J, Ringbauer H, Sikora M, McColl H, Pino-Yanes M, Ferrer MH, Bustamante CD, Fregel R. The genomic history of the indigenous people of the Canary Islands. Nat Commun 2023; 14:4641. [PMID: 37582830 PMCID: PMC10427657 DOI: 10.1038/s41467-023-40198-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
The indigenous population of the Canary Islands, which colonized the archipelago around the 3rd century CE, provides both a window into the past of North Africa and a unique model to explore the effects of insularity. We generate genome-wide data from 40 individuals from the seven islands, dated between the 3rd-16rd centuries CE. Along with components already present in Moroccan Neolithic populations, the Canarian natives show signatures related to Bronze Age expansions in Eurasia and trans-Saharan migrations. The lack of gene flow between islands and constant or decreasing effective population sizes suggest that populations were isolated. While some island populations maintained relatively high genetic diversity, with the only detected bottleneck coinciding with the colonization time, other islands with fewer natural resources show the effects of insularity and isolation. Finally, consistent genetic differentiation between eastern and western islands points to a more complex colonization process than previously thought.
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Affiliation(s)
- Javier G Serrano
- Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Alejandra C Ordóñez
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Jonathan Santana
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Elías Sánchez-Cañadillas
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Matilde Arnay
- Bioanthropology: Paleopathology, Diet and Nutrition in Ancient Populations Group, Department of Prehistory, Anthropology and Ancient History, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Amelia Rodríguez-Rodríguez
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Jacob Morales
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Javier Velasco-Vázquez
- Servicio de Patrimonio Histórico, Cabildo de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | | | | | | | - Juan Carlos Hernández
- Museo Arqueológico de La Gomera, San Sebastián de La Gomera, Santa Cruz de Tenerife, Spain
| | | | - Jorge Pais
- Museo Arqueológico Benahoarita, Los Llanos de Aridane, Santa Cruz de Tenerife, Spain
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Mariano Hernández Ferrer
- Molecular Genetics and Biodiversity Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Rosa Fregel
- Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.
- Department of Genetics, Stanford University, Stanford, CA, USA.
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2
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Goodspeed K, Mosca LR, Weitzel NC, Horning K, Simon EW, Pfalzer AC, Xia M, Langer K, Freed A, Bone M, Picone M, Bichell TJV. A draft conceptual model of SLC6A1 neurodevelopmental disorder. Front Neurosci 2023; 16:1026065. [PMID: 36741059 PMCID: PMC9893116 DOI: 10.3389/fnins.2022.1026065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/05/2022] [Indexed: 01/21/2023] Open
Abstract
Introduction SLC6A1 Neurodevelopmental Disorder (SLC6A1-NDD), first described in 2015, is a rare syndrome caused by a mutation in the SLC6A1 gene which encodes for the GABA Transporter 1 (GAT-1) protein. Epilepsy is one of the most common symptoms in patients and is often the primary treatment target, though the severity of epilepsy is variable. The impact of seizures and other symptoms of SLC6A1-NDD on patients and caregivers is wide-ranging and has not been described in a formal disease concept study. Methods A literature search was performed using the simple search term, "SLC6A1." Papers published before 2015, and those which did not describe the human neurodevelopmental disorder were removed from analysis. Open-ended interviews on lived experiences were conducted with two patient advocate key opinion leaders. An analysis of de-identified conversations between families of people with SLC6A1-NDD on social media was performed to quantify topics of concern. Results Published literature described symptoms in all of the following domains: neurological, visual, motor, cognitive, communication, behavior, gastrointestinal, sleep, musculo-skeletal, and emotional in addition to epilepsy. Key opinion leaders noted two unpublished features: altered hand use in infants, and developmental regression with onset of epilepsy. Analysis of social media interactions confirmed that the core symptoms of epilepsy and autistic traits were prominent concerns, but also demonstrated that other symptoms have a large impact on family life. Discussion For rare diseases, analysis of published literature is important, but may not be as comprehensive as that which can be gleaned from spontaneous interactions between families and through qualitative interviews. This report reflects our current understanding of the lived experience of SLC6A1-NDD. The discrepancy between the domains of disease reported in the literature and those discussed in patient conversations suggests that a formal qualitative interview-based disease concept study of SLC6A1-NDD is warranted.
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Affiliation(s)
- Kimberly Goodspeed
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, United States,*Correspondence: Kimberly Goodspeed,
| | - Lindsay R. Mosca
- College of Arts and Sciences, Vanderbilt University, Nashville, TN, United States
| | - Nicole C. Weitzel
- College of Arts and Sciences, Vanderbilt University, Nashville, TN, United States
| | | | - Elijah W. Simon
- College of Arts and Sciences, Vanderbilt University, Nashville, TN, United States
| | | | - Maya Xia
- COMBINEDBrain, Brentwood, TN, United States
| | - Katherine Langer
- College of Arts and Sciences, Vanderbilt University, Nashville, TN, United States
| | | | - Megan Bone
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Maria Picone
- TREND Community, Philadelphia, PA, United States
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3
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García-Olivares V, Rubio-Rodríguez LA, Muñoz-Barrera A, Díaz-de Usera A, Jáspez D, Iñigo-Campos A, Rodríguez Pérez MDC, Cabrera de León A, Lorenzo-Salazar JM, González-Montelongo R, Cabrera VM, Flores C. Digging into the admixture strata of current-day Canary Islanders based on mitogenomes. iScience 2022; 26:105907. [PMID: 36647378 PMCID: PMC9840145 DOI: 10.1016/j.isci.2022.105907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/18/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
The conquest of the Canary Islands by Europeans began at the beginning of the 15th century and culminated in 1496 with the surrender of the aborigines. The collapse of the aboriginal population during the conquest and the arrival of settlers caused a drastic change in the demographic composition of the archipelago. To shed light on this historical process, we analyzed 896 mitogenomes of current inhabitants from the seven main islands. Our findings confirm the continuity of aboriginal maternal contributions and the persistence of their genetic footprints in the current population, even at higher levels (>60% on average) than previously evidenced. Moreover, the age estimates for most autochthonous founder lineages support a first aboriginal arrival to the islands at the beginning of the first millennium. We also revealed for the first time that the main recognizable genetic influences from Europe are from Portuguese and Galicians.
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Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain,Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - Antonio Cabrera de León
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain,Área de Medicina Preventiva y Salud Pública, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain,Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | | | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain,Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain,Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain,Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Las Palmas de Gran Canaria, Spain,Corresponding author
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4
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Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders. Sci Rep 2022; 12:16132. [PMID: 36168029 PMCID: PMC9514705 DOI: 10.1038/s41598-022-20442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
The current inhabitants of the Canary Islands have a unique genetic makeup in the European diversity landscape due to the existence of African footprints from recent admixture events, especially of North African components (> 20%). The underrepresentation of non-Europeans in genetic studies and the sizable North African ancestry, which is nearly absent from all existing catalogs of worldwide genetic diversity, justify the need to develop CIRdb, a population-specific reference catalog of natural genetic variation in the Canary Islanders. Based on array genotyping of the selected unrelated donors and comparisons against available datasets from European, sub-Saharan, and North African populations, we illustrate the intermediate genetic differentiation of Canary Islanders between Europeans and North Africans and the existence of within-population differences that are likely driven by genetic isolation. Here we describe the overall design and the methods that are being implemented to further develop CIRdb. This resource will help to strengthen the implementation of Precision Medicine in this population by contributing to increase the diversity in genetic studies. Among others, this will translate into improved ability to fine map disease genes and simplify the identification of causal variants and estimate the prevalence of unattended Mendelian diseases.
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5
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Mendoza-Alvarez A, Tosco-Herrera E, Muñoz-Barrera A, Rubio-Rodríguez LA, Alonso-Gonzalez A, Corrales A, Iñigo-Campos A, Almeida-Quintana L, Martin-Fernandez E, Martinez-Beltran D, Perez-Rodriguez E, Callero A, Garcia-Robaina JC, González-Montelongo R, Marcelino-Rodriguez I, Lorenzo-Salazar JM, Flores C. A catalog of the genetic causes of hereditary angioedema in the Canary Islands (Spain). Front Immunol 2022; 13:997148. [PMID: 36203598 PMCID: PMC9531158 DOI: 10.3389/fimmu.2022.997148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Hereditary angioedema (HAE) is a rare disease where known causes involve C1 inhibitor dysfunction or dysregulation of the kinin cascade. The updated HAE management guidelines recommend performing genetic tests to reach a precise diagnosis. Unfortunately, genetic tests are still uncommon in the diagnosis routine. Here, we characterized for the first time the genetic causes of HAE in affected families from the Canary Islands (Spain). Whole-exome sequencing data was obtained from 41 affected patients and unaffected relatives from 29 unrelated families identified in the archipelago. The Hereditary Angioedema Database Annotation (HADA) tool was used for pathogenicity classification and causal variant prioritization among the genes known to cause HAE. Manual reclassification of prioritized variants was used in those families lacking known causal variants. We detected a total of eight different variants causing HAE in this patient series, affecting essentially SERPING1 and F12 genes, one of them being a novel SERPING1 variant (c.686-12A>G) with a predicted splicing effect which was reclassified as likely pathogenic in one family. Altogether, the diagnostic yield by assessing previously reported causal genes and considering variant reclassifications according to the American College of Medical Genetics guidelines reached 66.7% (95% Confidence Interval [CI]: 30.1-91.0) in families with more than one affected member and 10.0% (95% CI: 1.8-33.1) among cases without family information for the disease. Despite the genetic causes of many patients remain to be identified, our results reinforce the need of genetic tests as first-tier diagnostic tool in this disease, as recommended by the international WAO/EAACI guidelines for the management of HAE.
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Affiliation(s)
| | - Eva Tosco-Herrera
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Adrian Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Aitana Alonso-Gonzalez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Lourdes Almeida-Quintana
- Allergy Service, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Elena Martin-Fernandez
- Allergy Service, Hospital Universitario Dr. Molina Orosa, Las Palmas de Gran Canaria, Spain
| | - Dara Martinez-Beltran
- Allergy Service, Hospital Universitario Insular-Materno Infantil, Las Palmas de Gran Canaria, Spain
| | - Eva Perez-Rodriguez
- Allergy Service, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Ariel Callero
- Allergy Service, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose C. Garcia-Robaina
- Allergy Service, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Itahisa Marcelino-Rodriguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Public Health and Preventive Medicine Area, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- *Correspondence: Carlos Flores,
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6
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Hernandez-Beeftink T, Marcelino-Rodríguez I, Guillen-Guio B, Rodríguez-Pérez H, Lorenzo-Salazar JM, Corrales A, Díaz-de Usera A, González-Montelongo R, Domínguez D, Espinosa E, Villar J, Flores C. Admixture Mapping of Sepsis in European Individuals With African Ancestries. Front Med (Lausanne) 2022; 9:754440. [PMID: 35345767 PMCID: PMC8957104 DOI: 10.3389/fmed.2022.754440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/24/2022] [Indexed: 11/30/2022] Open
Abstract
Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction. Although the ancestral genetic background is a relevant factor for sepsis susceptibility, there is a lack of studies using the genetic singularities of a recently admixed population to identify loci involved in sepsis susceptibility. Here we aimed to discover new sepsis loci by completing the first admixture mapping study of sepsis in Canary Islanders, leveraging their distinctive genetic makeup as a mixture of Europeans and African ancestries. We used a case-control approach and inferred local ancestry blocks from genome-wide data from 113,414 polymorphisms genotyped in 343 patients with sepsis and 410 unrelated controls, all ascertained for grandparental origin in the Canary Islands (Spain). Deviations in local ancestries between cases and controls were tested using logistic regressions, followed by fine-mapping analyses based on imputed genotypes, in silico functional assessments, and gene expression analysis centered on the region of interest. The admixture mapping analysis detected that local European ancestry in a locus spanning 1.2 megabases of chromosome 8p23.1 was associated with sepsis (lowest p = 1.37 × 10−4; Odds Ratio [OR] = 0.51; 95%CI = 0.40–0.66). Fine-mapping studies prioritized the variant rs13249564 within intron 1 of MFHAS1 gene associated with sepsis (p = 9.94 × 10−4; OR = 0.65; 95%CI = 0.50–0.84). Functional and gene expression analyses focused on 8p23.1 allowed us to identify alternative genes with possible biological plausibility such as defensins, which are well-known effector molecules of innate immunity. By completing the first admixture mapping study of sepsis, our results revealed a new genetic locus (8p23.1) harboring a number of genes with plausible implications in sepsis susceptibility.
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Affiliation(s)
- Tamara Hernandez-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Research Unit, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Itahisa Marcelino-Rodríguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - David Domínguez
- Department of Anesthesiology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Elena Espinosa
- Department of Anesthesiology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jesús Villar
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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7
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Nóvoa-Medina Y, Pavlovic-Nesic S, González-Martín JM, Hernández-Betancor A, López S, Domínguez-García A, Quinteiro-Domínguez S, Cabrera M, De La Cuesta A, Caballero-Fernández E, González-Perera MA, De Miguel-Martínez I, Ogle GD, Wägner AM. Role of the SARS-CoV-2 virus in the appearance of new onset type 1 diabetes mellitus in children in Gran Canaria, Spain. J Pediatr Endocrinol Metab 2022; 35:393-397. [PMID: 35026884 DOI: 10.1515/jpem-2021-0727] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/01/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES It has been hypothesized that SARS-CoV-2 may play a role in the development of different forms of diabetes mellitus (DM). The Canary Islands have the highest incidence of type 1 DM (T1DM) reported in Spain (30-35/100,000 children under 14 years/year). In 2020-2021 we observed the highest incidence so far on the island of Gran Canaria, as a result of which we decided to evaluate the possible role of COVID-19 in the increased number of onsets. METHODS We examined the presence of IgG antibodies against SARS-CoV-2 in children with new onset T1DM between October 2020 and August 2021. We compared recent T1DM incidence with that of the previous 10 years. RESULTS Forty-two patients were diagnosed with T1DM (48.1/100,000 patients/year), representing a nonsignificant 25.7% increase from the expected incidence. Of the 33 patients who consented to the study, 32 presented negative IgG values, with only one patient reflecting undiagnosed past infection. Forty-four percent of patients presented with ketoacidosis at onset, which was similar to previous years. CONCLUSIONS We conclude that there is no direct relationship between the increased incidence of T1DM and SARS-CoV-2 in the region. The COVID-19 pandemic did not result in an increased severity of T1DM presentation.
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Affiliation(s)
- Yeray Nóvoa-Medina
- Pediatric Endocrinology Unit, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain.,Asociación Canaria para la Investigación Pediátrica (ACIP canarias), Canary Islands, Spain.,Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Canary Islands, Spain
| | - Svetlana Pavlovic-Nesic
- Pediatric Department, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
| | | | - Araceli Hernández-Betancor
- Microbiology Department, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
| | - Sara López
- Pediatric Endocrinology Unit, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
| | - Angela Domínguez-García
- Pediatric Endocrinology Unit, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
| | - Sofía Quinteiro-Domínguez
- Pediatric Endocrinology Unit, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
| | - María Cabrera
- Pediatric Endocrinology Unit, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
| | - Araceli De La Cuesta
- Pediatric Endocrinology Unit, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
| | - Elisabeth Caballero-Fernández
- Pediatric Endocrinology Unit, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
| | - María A González-Perera
- Pediatric Endocrinology Unit, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
| | - Isabel De Miguel-Martínez
- Microbiology Department, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
| | - Graham D Ogle
- Life for a Child Program, Diabetes NSW & ACT, Sydney, Australia
| | - Ana M Wägner
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria (ULPGC), Canary Islands, Spain.,Endocrinology Department, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de GC, Canary Islands, Spain
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8
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Suarez-Pajes E, Díaz-García C, Rodríguez-Pérez H, Lorenzo-Salazar JM, Marcelino-Rodríguez I, Corrales A, Zheng X, Callero A, Perez-Rodriguez E, Garcia-Robaina JC, González-Montelongo R, Flores C, Guillen-Guio B. Targeted analysis of genomic regions enriched in African ancestry reveals novel classical HLA alleles associated with asthma in Southwestern Europeans. Sci Rep 2021; 11:23686. [PMID: 34880287 PMCID: PMC8654850 DOI: 10.1038/s41598-021-02893-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
Despite asthma has a considerable genetic component, an important proportion of genetic risks remain unknown, especially for non-European populations. Canary Islanders have the largest African genetic ancestry observed among Southwestern Europeans and the highest asthma prevalence in Spain. Here we examined broad chromosomal regions previously associated with an excess of African genetic ancestry in Canary Islanders, with the aim of identifying novel risk variants associated with asthma susceptibility. In a two-stage cases-control study, we revealed a variant within HLA-DQB1 significantly associated with asthma risk (rs1049213, meta-analysis p = 1.30 × 10–7, OR [95% CI] = 1.74 [1.41–2.13]) previously associated with asthma and broad allergic phenotype. Subsequent fine-mapping analyses of classical HLA alleles revealed a novel allele significantly associated with asthma protection (HLA-DQA1*01:02, meta-analysis p = 3.98 × 10–4, OR [95% CI] = 0.64 [0.50–0.82]) that had been linked to infectious and autoimmune diseases, and peanut allergy. HLA haplotype analyses revealed a novel haplotype DQA1*01:02-DQB1*06:04 conferring asthma protection (meta-analysis p = 4.71 × 10–4, OR [95% CI] = 0.47 [0.29– 0.73]).
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Affiliation(s)
- Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Claudio Díaz-García
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Itahisa Marcelino-Rodríguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ariel Callero
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Eva Perez-Rodriguez
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose C Garcia-Robaina
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain. .,Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain. .,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain. .,Department of Health Sciences, University of Leicester, Leicester, UK.
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9
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Mendoza-Alvarez A, Marcelino-Rodriguez I, Almeida-Quintana L, Martin-Fernandez E, Martinez-Beltran D, Almeida-Sanchez Z, Cruz-Niesvara D, Hernández-Santana G, Garcia-Robaina JC, Flores C, Callero A. First Census of Patients with Hereditary Angioedema in the Canary Islands. J Clin Med 2021; 10:jcm10204711. [PMID: 34682833 PMCID: PMC8540601 DOI: 10.3390/jcm10204711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022] Open
Abstract
Hereditary angioedema (HAE) is a rare genetic condition whose main symptoms are recurrent swelling in the skin, mucosa, and internal organs. Recent studies suggested that the regulation of the inflammatory response and the complement cascade are two of the pathways significantly enriched in the Canary Islands, Spain. Here, we describe the first HAE patient series in this region. Forty-one patients (33 F, 8 M) and nine healthy relatives belonging to twenty-nine families were recruited for this study, obtaining their clinical and demographic features using a data collection form, as well as blood samples for biochemical analysis. The mean age of patients was 36.8 years (ranging from 4 to 72 years). Positive family history of HAE was reported in 13 patients (32.5%), and a mean diagnosis delay of 7.9 (±12.5) years was estimated, ranging from months to 50 years. Cutaneous edema was the most common symptom (53.6%), while airway symptoms was present in 11 patients. Prophylactic treatment was indicated for 23 patients, while 14 also require on-demand rescue treatment. We estimate a minimum prevalence of 1.25:100,000 for HAE due to C1-INH deficiency or dysfunction in the Canary Islands, which is higher than the estimates for mainland Spanish populations. HAE continues to be a disease poorly recognized by health care professionals due to its confusing symptoms, leading to longer diagnosis delay. Altogether, the evidence reinforces the need for a rapid and accurate diagnosis and precision medicine-based studies to improve the patient's quality of life.
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Affiliation(s)
- Alejandro Mendoza-Alvarez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain; (A.M.-A.); (I.M.-R.); (C.F.)
| | - Itahisa Marcelino-Rodriguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain; (A.M.-A.); (I.M.-R.); (C.F.)
| | | | | | - Dara Martinez-Beltran
- Allergy Service, Hospital Universitario Insular-Materno Infantil, 35016 Las Palmas, Spain;
| | | | - David Cruz-Niesvara
- Allergy Service, Hospital General de Fuerteventura Virgen de la Peña, 35600 Las Palmas, Spain;
| | | | - Jose C. Garcia-Robaina
- Allergy Service, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain;
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain; (A.M.-A.); (I.M.-R.); (C.F.)
- Genomics Division, Instituto Tecnológico y de Energías Renovables, 38600 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ariel Callero
- Allergy Service, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain;
- Correspondence: ; Tel.: +34-922-602220
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10
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Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases. Int J Mol Sci 2021; 22:ijms22136962. [PMID: 34203440 PMCID: PMC8269095 DOI: 10.3390/ijms22136962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Admixed populations arise when two or more ancestral populations interbreed. As a result of this admixture, the genome of admixed populations is defined by tracts of variable size inherited from these parental groups and has particular genetic features that provide valuable information about their demographic history. Diverse methods can be used to derive the ancestry apportionment of admixed individuals, and such inferences can be leveraged for the discovery of genetic loci associated with diseases and traits, therefore having important biomedical implications. In this review article, we summarize the most common methods of global and local genetic ancestry estimation and discuss the use of admixture mapping studies in human diseases.
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11
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Hernández CL, Pita G, Cavadas B, López S, Sánchez-Martínez LJ, Dugoujon JM, Novelletto A, Cuesta P, Pereira L, Calderón R. Human Genomic Diversity Where the Mediterranean Joins the Atlantic. Mol Biol Evol 2021; 37:1041-1055. [PMID: 31816048 PMCID: PMC7086172 DOI: 10.1093/molbev/msz288] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Throughout the past few years, a lively debate emerged about the timing and magnitude of the human migrations between the Iberian Peninsula and the Maghreb. Several pieces of evidence, including archaeological, anthropological, historical, and genetic data, have pointed to a complex and intermingled evolutionary history in the western Mediterranean area. To study to what extent connections across the Strait of Gibraltar and surrounding areas have shaped the present-day genomic diversity of its populations, we have performed a screening of 2.5 million single-nucleotide polymorphisms in 142 samples from southern Spain, southern Portugal, and Morocco. We built comprehensive data sets of the studied area and we implemented multistep bioinformatic approaches to assess population structure, demographic histories, and admixture dynamics. Both local and global ancestry inference showed an internal substructure in the Iberian Peninsula, mainly linked to a differential African ancestry. Western Iberia, from southern Portugal to Galicia, constituted an independent cluster within Iberia characterized by an enriched African genomic input. Migration time modeling showed recent historic dates for the admixture events occurring both in Iberia and in the North of Africa. However, an integrative vision of both paleogenomic and modern DNA data allowed us to detect chronological transitions and population turnovers that could be the result of transcontinental migrations dating back from Neolithic times. The present contribution aimed to fill the gaps in the modern human genomic record of a key geographic area, where the Mediterranean and the Atlantic come together.
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Affiliation(s)
- Candela L Hernández
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Bruno Cavadas
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Saioa López
- UCL Cancer Institute, London, United Kingdom
| | - Luis J Sánchez-Martínez
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Jean-Michel Dugoujon
- CNRS UMR 5288 Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, Toulouse, France
| | | | - Pedro Cuesta
- Centro de Proceso de Datos, Universidad Complutense, Madrid, Spain
| | - Luisa Pereira
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Rosario Calderón
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense, Madrid, Spain
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12
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The incidence of skin melanoma in Gran Canaria (Canary Islands, Spain) is lower than expected in Southern Europe despite high-risk environmental conditions: an island-wide cross-sectional study. Cancer Causes Control 2021; 32:525-535. [PMID: 33646461 DOI: 10.1007/s10552-021-01403-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/29/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND The Canary Islands are a leading European touristic destination. The ultraviolet index (UVI) in the region is the highest in Spain, and similar to indexes registered in Australia and New Zealand, which hold the highest incidence of skin melanoma worldwide. Yet according to cancer registry data, the incidence in the Canary Islands in the late 1990s was the lowest in Spain (among the lowest in Europe) and about six times lower than in New Zealand. PURPOSE To analyze the incidence rates of skin melanoma in Gran Canaria island between 2007 and 2018. METHODS The study was based in the two centres of the Canary Islands' Healthcare Service centralizing melanoma care in Gran Canaria. We analyzed crude and age-standardized (ASR) incidence rates of invasive cutaneous melanoma for the period 2007-2018 following the inclusion criteria of the International Agency for Research on Cancer (IARC). Clinical and histological characteristics of melanoma patients were assessed. RESULTS A total of 1058 patients were included. The incidence rates obtained matched the latest available Canary Islands' cancer registry data, confirming its reliability (ASR, Segi-Doll world standard population: 6.4 cases per 100,000 habitants for 2008-2012). The incidence was also below the latest IARC predictions for Southern Europe (GLOBOCAN 2018). Histological characteristics of patients were similar to other Southern European series. CONCLUSIONS The incidence of skin melanoma in Gran Canaria is unexpectedly low for a Southern European population exposed to such a high UVI. Further research in the Canary Islands could provide insight into a better understanding of melanoma pathogenesis.
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13
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Guillen-Guio B, Hernández-Beeftink T, Marcelino-Rodríguez I, Rodríguez-Pérez H, Lorenzo-Salazar JM, Espinilla-Peña M, Corrales A, Pino-Yanes M, Callero A, Perez-Rodriguez E, Villar J, González-Montelongo R, Flores C. Admixture mapping of asthma in southwestern Europeans with North African ancestry influences. Am J Physiol Lung Cell Mol Physiol 2020; 318:L965-L975. [PMID: 32186396 DOI: 10.1152/ajplung.00344.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The prevalence of asthma symptoms in Canary Islanders, a southwestern European population from Spain, is almost three times higher than the country average. Because the genetic risks identified so far explain <5% of asthma heritability, here we aimed to discover new asthma loci by completing the first admixture mapping study in Canary Islanders leveraging their distinctive genetic makeup, where significant northwest African influences coexist in the European genetic diversity landscape. A 2-stage study was conducted in 1,491 unrelated individuals self-declaring having a Canary Islands origin for the 4 grandparents. Local ancestry estimates were obtained for the shared positions with reference data from putative ancestral populations from Europe, North Africa, and sub-Saharan Africa. Case-control deviations in local ancestry were tested for each ancestry separately using logistic regressions adjusted for principal components, followed by fine-mapping analyses based on imputed genotypes and analyses of the likely deleterious exonic variants. The admixture mapping analysis of asthma detected that local North African ancestry in a locus spanning 365 kb of chromosome 16q23.3 was associated with asthma risk at study-wide significance [lowest P = 1.12 × 10-4; odds ratio (OR) = 2.05; 95% confidence interval (CI) = 1.41-3.00]. Fine-mapping studies identified a variant associated with asthma, and results were replicated in independent samples (rs3852738, OR = 1.34; 95% CI = 1.13-1.59, P = 7.58 × 10-4). Whole exome sequencing data from a subset of individuals revealed an enrichment of likely deleterious variants among asthma cases in 16q23.3, particularly in the phospholipase Cγ2 (PLCG2) gene (P = 3.67 × 10-4). By completing the first mapping study of asthma in admixed populations from Europe, our results revealed a new plausible asthma locus.
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Affiliation(s)
- Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Tamara Hernández-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Research Unit, Hospital Universitario de Gran Canaria Doctor Negrín, Las Palmas de Gran Canaria, Spain
| | - Itahisa Marcelino-Rodríguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Marta Espinilla-Peña
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Pino-Yanes
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Ariel Callero
- Allergy Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Eva Perez-Rodriguez
- Allergy Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jesús Villar
- Research Unit, Hospital Universitario de Gran Canaria Doctor Negrín, Las Palmas de Gran Canaria, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
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14
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Guillen-Guio B, Lorenzo-Salazar JM, Ma SF, Hou PC, Hernandez-Beeftink T, Corrales A, García-Laorden MI, Jou J, Espinosa E, Muriel A, Domínguez D, Lorente L, Martín MM, Rodríguez-Gallego C, Solé-Violán J, Ambrós A, Carriedo D, Blanco J, Añón JM, Reilly JP, Jones TK, Ittner CA, Feng R, Schöneweck F, Kiehntopf M, Noth I, Scholz M, Brunkhorst FM, Scherag A, Meyer NJ, Villar J, Flores C. Sepsis-associated acute respiratory distress syndrome in individuals of European ancestry: a genome-wide association study. THE LANCET RESPIRATORY MEDICINE 2020; 8:258-266. [PMID: 31982041 DOI: 10.1016/s2213-2600(19)30368-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/25/2019] [Accepted: 08/07/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS) is a lung inflammatory process caused mainly by sepsis. Most previous studies that identified genetic risks for ARDS focused on candidates with biological relevance. We aimed to identify novel genetic variants associated with ARDS susceptibility and to provide complementary functional evidence of their effect in gene regulation. METHODS We did a case-control genome-wide association study (GWAS) of 1935 European individuals, using patients with sepsis-associated ARDS as cases and patients with sepsis without ARDS as controls. The discovery stage included 672 patients admitted into a network of Spanish intensive care units between January, 2002, and January, 2017. The replication stage comprised 1345 individuals from two independent datasets from the MESSI cohort study (Sep 22, 2008-Nov 30, 2017; USA) and the VISEP (April 1, 2003-June 30, 2005) and MAXSEP (Oct 1, 2007-March 31, 2010) trials of the SepNet study (Germany). Results from discovery and replication stages were meta-analysed to identify association signals. We then used RNA sequencing data from lung biopsies, in-silico analyses, and luciferase reporter assays to assess the functionallity of associated variants. FINDINGS We identified a novel genome-wide significant association with sepsis-associated ARDS susceptibility (rs9508032, odds ratio [OR] 0·61, 95% CI 0·41-0·91, p=5·18 × 10-8) located within the Fms-related tyrosine kinase 1 (FLT1) gene, which encodes vascular endothelial growth factor receptor 1 (VEGFR-1). The region containing the sentinel variant and its best proxies acted as a silencer for the FLT1 promoter, and alleles with protective effects in ARDS further reduced promoter activity (p=0·0047). A literature mining of all previously described ARDS genes validated the association of vascular endothelial growth factor A (VEGFA; OR 0·55, 95% CI 0·41-0·73; p=4·69 × 10-5). INTERPRETATION A common variant within the FLT1 gene is associated with sepsis-associated ARDS. Our findings support a role for the vascular endothelial growth factor signalling pathway in ARDS pathogenesis and identify VEGFR-1 as a potential therapeutic target. FUNDING Instituto de Salud Carlos III, European Regional Development Funds, Instituto Tecnológico y de Energías Renovables.
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Affiliation(s)
- Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Shwu-Fan Ma
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Pei-Chi Hou
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Tamara Hernandez-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain; Research Unit, Hospital Universitario de Gran Canaria Dr Negrín, Las Palmas de Gran Canaria, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - M Isabel García-Laorden
- Research Unit, Hospital Universitario de Gran Canaria Dr Negrín, Las Palmas de Gran Canaria, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Jonathan Jou
- University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Elena Espinosa
- Department of Anesthesiology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Arturo Muriel
- Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - David Domínguez
- Department of Anesthesiology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Leonardo Lorente
- Intensive Care Unit, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain
| | - María M Martín
- Intensive Care Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Carlos Rodríguez-Gallego
- Department of Immunology, Hospital Universitario de Gran Canaria Dr Negrín, Las Palmas de Gran Canaria, Spain
| | - Jordi Solé-Violán
- Intensive Care Unit, Hospital Universitario de Gran Canaria Dr Negrín, Las Palmas de Gran Canaria, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Alfonso Ambrós
- Intensive Care Unit, Hospital General de Ciudad Real, Ciudad Real, Spain
| | - Demetrio Carriedo
- Intensive Care Unit, Complejo Hospitalario Universitario de León, León, Spain
| | - Jesús Blanco
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - José M Añón
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Intensive Care Unit, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - John P Reilly
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Tiffanie K Jones
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Caroline Ag Ittner
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Rui Feng
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia PA, USA
| | - Franziska Schöneweck
- Integrated Research and Treatment Center, Jena University Hospital, Jena, Germany
| | - Michael Kiehntopf
- Center for Sepsis Control and Care, Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany; Integrated Biobank Jena, Jena University Hospital, Jena, Germany
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Frank M Brunkhorst
- Center for Clinical Studies, Jena University Hospital, Jena, Germany; Paul-Martini-Clinical Sepsis Research Unit, Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - André Scherag
- Integrated Research and Treatment Center, Jena University Hospital, Jena, Germany; Institute of Medical Statistics, Computer and Data Sciences, Jena University Hospital, Jena, Germany
| | - Nuala J Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Jesús Villar
- Research Unit, Hospital Universitario de Gran Canaria Dr Negrín, Las Palmas de Gran Canaria, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Keenan Research Center for Biomedical Sciences at the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain; Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
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15
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Fregel R, Ordóñez AC, Santana-Cabrera J, Cabrera VM, Velasco-Vázquez J, Alberto V, Moreno-Benítez MA, Delgado-Darias T, Rodríguez-Rodríguez A, Hernández JC, Pais J, González-Montelongo R, Lorenzo-Salazar JM, Flores C, Cruz-de-Mercadal MC, Álvarez-Rodríguez N, Shapiro B, Arnay M, Bustamante CD. Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands. PLoS One 2019; 14:e0209125. [PMID: 30893316 PMCID: PMC6426200 DOI: 10.1371/journal.pone.0209125] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/15/2019] [Indexed: 12/30/2022] Open
Abstract
The Canary Islands’ indigenous people have been the subject of substantial archaeological, anthropological, linguistic and genetic research pointing to a most probable North African Berber source. However, neither agreement about the exact point of origin nor a model for the indigenous colonization of the islands has been established. To shed light on these questions, we analyzed 48 ancient mitogenomes from 25 archaeological sites from the seven main islands. Most lineages observed in the ancient samples have a Mediterranean distribution, and belong to lineages associated with the Neolithic expansion in the Near East and Europe (T2c, J2a, X3a…). This phylogeographic analysis of Canarian ancient mitogenomes, the first of its kind, shows that some lineages are restricted to Central North Africa (H1cf, J2a2d and T2c1d3), while others have a wider distribution, including both West and Central North Africa, and, in some cases, Europe and the Near East (U6a1a1, U6a7a1, U6b, X3a, U6c1). In addition, we identify four new Canarian-specific lineages (H1e1a9, H4a1e, J2a2d1a and L3b1a12) whose coalescence dates correlate with the estimated time for the colonization of the islands (1st millennia CE). Additionally, we observe an asymmetrical distribution of mtDNA haplogroups in the ancient population, with certain haplogroups appearing more frequently in the islands closer to the continent. This reinforces results based on modern mtDNA and Y-chromosome data, and archaeological evidence suggesting the existence of two distinct migrations. Comparisons between insular populations show that some populations had high genetic diversity, while others were probably affected by genetic drift and/or bottlenecks. In spite of observing interinsular differences in the survival of indigenous lineages, modern populations, with the sole exception of La Gomera, are homogenous across the islands, supporting the theory of extensive human mobility after the European conquest.
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Affiliation(s)
- Rosa Fregel
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- * E-mail:
| | - Alejandra C. Ordóñez
- Department of Prehistory, Anthropology and Ancient History, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | | | - Vicente M. Cabrera
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Javier Velasco-Vázquez
- Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Verónica Alberto
- Tibicena Arqueología y Patrimonio, Las Palmas de Gran Canaria, Spain
| | | | | | - Amelia Rodríguez-Rodríguez
- Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | | | - Jorge Pais
- Museo Arqueológico Benahoarita, Los Llanos de Aridane, Spain
| | | | | | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Granadilla, Spain
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Matilde Arnay
- Department of Prehistory, Anthropology and Ancient History, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
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