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Fonseca H, da Silva TM, Saraiva M, Santolalla ML, Sant’Anna HP, Araujo NM, Lima NP, Rios R, Tarazona-Santos E, Horta BL, Cruz A, Barreto ML, Figueiredo CA. Genomic Regions 10q22.2, 17q21.31, and 2p23.1 Can Contribute to a Lower Lung Function in African Descent Populations. Genes (Basel) 2020; 11:E1047. [PMID: 32899814 PMCID: PMC7565985 DOI: 10.3390/genes11091047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/02/2022] Open
Abstract
Accumulated evidence supports the contribution of genetic factors in modulating airway function, especially ancestry. We investigated whether genetic polymorphisms can affect lung function in a mixed Brazilian child population using the admixture mapping strategy through RFMix software version 1.5.4 (Stanford University, Stanford, CA, USA), followed by fine mapping, to identify regions whereby local African or European ancestry is associated with lung function measured by the forced expiratory volume in the first second (FEV1)/forced vital capacity (FVC) ratio, an indicator of airway obstruction. The research cohort included 958 individuals aged 4 to 11 years enrolled in the SCAALA (Social Change, Asthma, Allergy in Latin America) Program. We identified that African ancestry at 17q21.31, 10q22.2, and 2p23.1 regions was associated with lower lung function measured by FEV1/FVC p < 1.9 × 10-4. In contrast, European ancestry at 17q21.31 showed an opposite effect. Fine mapping pointed out 5 single nucleotide polymorphisms (SNPs) also associated in our replication cohort (rs10999948, rs373831475, rs8068257, rs6744555, and rs1520322). Our results suggest that genomic regions associated with ancestry may contribute to differences in lung function measurements in African American children in Brazil replicated in a cohort of Brazilian adults. The analysis strategy used in this work is especially important for phenotypes, such as lung function, which has considerable disparities in terms of measurements across different populations.
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Affiliation(s)
- Héllen Fonseca
- Programa de Pós Graduação em Imunologia (PPGIm), Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador 40140-100, BA, Brazil; (H.F.); (M.S.); (R.R.)
| | - Thiago M. da Silva
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié 45206-190, BA, Brazil;
| | - Mariana Saraiva
- Programa de Pós Graduação em Imunologia (PPGIm), Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador 40140-100, BA, Brazil; (H.F.); (M.S.); (R.R.)
| | - Meddly L. Santolalla
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.L.S.); (H.P.S.); (N.M.A.); (E.T.-S.)
| | - Hanaisa P. Sant’Anna
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.L.S.); (H.P.S.); (N.M.A.); (E.T.-S.)
| | - Nathalia M. Araujo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.L.S.); (H.P.S.); (N.M.A.); (E.T.-S.)
| | - Natália P. Lima
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas 96020-220, Rio Grande do Sul, Brazil; (N.P.L.); (B.L.H.)
| | - Raimon Rios
- Programa de Pós Graduação em Imunologia (PPGIm), Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador 40140-100, BA, Brazil; (H.F.); (M.S.); (R.R.)
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.L.S.); (H.P.S.); (N.M.A.); (E.T.-S.)
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas 96020-220, Rio Grande do Sul, Brazil; (N.P.L.); (B.L.H.)
| | - Alvaro Cruz
- ProAR, Faculdade de Medicina, Universidade Federal da Bahia (UFBA), Salvador 40060-330, BA, Brazil;
| | - Mauricio L. Barreto
- Centro de Integração de dados e Conhecimentos para Saúde (CIDACS), Fiocruz, Salvador 41745-715, BA, Brazil;
| | - Camila A. Figueiredo
- Departamento de Bio-Regulação, Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador 40110-902, BA, Brazil
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da Silva TM, Fiaccone RL, Kehdy FSG, Tarazona-Santos E, Rodrigues LC, Costa GNO, Figueiredo CA, Dos Santos DN, Feitosa CA, Fattore GL, Santos LM, Alcantara-Neves NM, Cruz ÁA, Barreto ML. African biogeographical ancestry, atopic and non-atopic asthma and atopy: A study in Latin American children. Pediatr Pulmonol 2019; 54:125-132. [PMID: 30548437 DOI: 10.1002/ppul.24213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/03/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genetic variants underlying African ancestry have been suggested be implicated in the ethnic-racial inequalities reported for asthma and allergies. OBJECTIVES To investigate the association between individual African ancestry and asthma symptoms, atopic and non-atopic asthma, and atopy in children. METHODS A cross-sectional study encompassing 1190 individuals was conducted. African biogeographic ancestry was estimated using 370 539 genome-wide SNPs. Serum levels of specific IgE were measured, and skin prick test (SPT) performed for the most common local aeroallergens. Information on asthma symptoms was obtained by applying the International Study of Allergy and Asthma in Childhood questionnaire. The associations between the proportion of individual African ancestry and the outcomes investigated were analyzed through multivariate models adjusted for socio-environmental variables, infections markers, and psychosocial factors. RESULTS Each 20% increase in the proportion of African ancestry was negatively associated with SPT reactivity (OR: 0.79, 95%CI: 0.66-0.96) and positively associated with asthma symptoms in non-atopic individuals (OR: 1.40, 95%CI: 1.03-1.89). We estimated that socioeconomic status and number of infections mediated 28.4% of the effect of African ancestry on SPT reactivity, while 20.2% of the effect on non-atopic asthma was explained by socioeconomic status and behavioral problems in children. CONCLUSIONS The negative association observed between African ancestry and atopy is most probably explained by unobserved environmental or social factors that covariate with ancestry. For non-atopic asthma, in turn, putative genetic variants of risk underlying African ancestry may play some role.
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Affiliation(s)
- Thiago M da Silva
- Institute of Collective Health, Federal University of Bahia, Salvador, Bahia, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Bahia, Brazil
| | - Rosemeire L Fiaccone
- Departamento de Estatística, Instituto de Matemática, Universidade Federal da Bahia, Salvador, Bahia, Brazil.,Center of Data and Knowledge Integration for Health, Instituto Gonçalo Muniz, Fundação Osvaldo Cruz, Salvador, Brazil
| | - Fernanda S G Kehdy
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de, Janeiro, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Laura C Rodrigues
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gustavo N O Costa
- Institute of Collective Health, Federal University of Bahia, Salvador, Bahia, Brazil.,Center of Data and Knowledge Integration for Health, Instituto Gonçalo Muniz, Fundação Osvaldo Cruz, Salvador, Brazil
| | - Camila A Figueiredo
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Darci N Dos Santos
- Institute of Collective Health, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Caroline A Feitosa
- Institute of Collective Health, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Gisel L Fattore
- Institute of Collective Health, Federal University of Bahia, Salvador, Bahia, Brazil.,Departamento de Salud Comunitaria, Universidad Nacional de Lanús, Buenos Aires, Argentina
| | - Leticia M Santos
- Institute of Collective Health, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | - Álvaro A Cruz
- ProAR-Center of Excellence in Asthma, Federal University of Bahia School of Medicine, Salvador, Brazil
| | - Maurício L Barreto
- Institute of Collective Health, Federal University of Bahia, Salvador, Bahia, Brazil.,Center of Data and Knowledge Integration for Health, Instituto Gonçalo Muniz, Fundação Osvaldo Cruz, Salvador, Brazil
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Costa GNO, Dudbridge F, Fiaccone RL, da Silva TM, Conceição JS, Strina A, Figueiredo CA, Magalhães WCS, Rodrigues MR, Gouveia MH, Kehdy FSG, Horimoto ARVR, Horta B, Burchard EG, Pino-Yanes M, Del Rio Navarro B, Romieu I, Hancock DB, London S, Lima-Costa MF, Pereira AC, Tarazona E, Rodrigues LC, Barreto ML. A genome-wide association study of asthma symptoms in Latin American children. BMC Genet 2015; 16:141. [PMID: 26635092 PMCID: PMC4669662 DOI: 10.1186/s12863-015-0296-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/17/2015] [Indexed: 01/14/2023] Open
Abstract
Background Asthma is a chronic disease of the airways and, despite the advances in the knowledge of associated genetic regions in recent years, their mechanisms have yet to be explored. Several genome-wide association studies have been carried out in recent years, but none of these have involved Latin American populations with a high level of miscegenation, as is seen in the Brazilian population. Methods 1246 children were recruited from a longitudinal cohort study in Salvador, Brazil. Asthma symptoms were identified in accordance with an International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire. Following quality control, 1 877 526 autosomal SNPs were tested for association with childhood asthma symptoms by logistic regression using an additive genetic model. We complemented the analysis with an estimate of the phenotypic variance explained by common genetic variants. Replications were investigated in independent Mexican and US Latino samples. Results Two chromosomal regions reached genome-wide significance level for childhood asthma symptoms: the 14q11 region flanking the DAD1 and OXA1L genes (rs1999071, MAF 0.32, OR 1.78, 95 % CI 1.45–2.18, p-value 2.83 × 10−8) and 15q22 region flanking the FOXB1 gene (rs10519031, MAF 0.04, OR 3.0, 95 % CI 2.02–4.49, p-value 6.68 × 10−8 and rs8029377, MAF 0.03, OR 2.49, 95 % CI 1.76–3.53, p-value 2.45 × 10−7). eQTL analysis suggests that rs1999071 regulates the expression of OXA1L gene. However, the original findings were not replicated in the Mexican or US Latino samples. Conclusions We conclude that the 14q11 and 15q22 regions may be associated with asthma symptoms in childhood. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0296-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gustavo N O Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil.
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
| | | | - Thiago M da Silva
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil.
| | | | - Agostino Strina
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil.
| | - Camila A Figueiredo
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.
| | - Wagner C S Magalhães
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Maira R Rodrigues
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Mateus H Gouveia
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Fernanda S G Kehdy
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | | | - Bernardo Horta
- Programa de Pós Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, Brazil.
| | | | - Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, USA.
| | - Blanca Del Rio Navarro
- Department of Health and Human Services, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
| | | | - Dana B Hancock
- Behavioral and Urban Health Program, Research Triangle Institute (RTI) International, Research Triangle Park, North Carolina, USA.
| | - Stephanie London
- Department of Health and Human Services, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
| | | | - Alexandre C Pereira
- Instituto de Pesquisas Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil.
| | - Eduardo Tarazona
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Laura C Rodrigues
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil. .,Centro de Pesquisa Gonçalo Muniz, Fundação Osvaldo Cruz, Salvador, Brazil.
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Castro DB, Pereira LB, Silva MVME, Silva BPD, Palermo BRZ, Carlos C, Belgini DR, Limache EEG, Lacerda GVJ, Nery MB, Gomes MB, Souza SSD, Silva TMD, Rodrigues VD, Paulino LC, Vicentini R, Ferraz LF, Ottoboni LM. High-quality draft genome sequence of Kocuria marina SO9-6, an actinobacterium isolated from a copper mine. Genom Data 2015; 5:34-5. [PMID: 26484219 PMCID: PMC4583624 DOI: 10.1016/j.gdata.2015.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/06/2015] [Accepted: 05/10/2015] [Indexed: 11/17/2022]
Abstract
An actinobacterial strain, designated SO9-6, was isolated from a copper iron sulfide mineral. The organism is Gram-positive, facultatively anaerobic, and coccoid. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Kocuria. Here, we report the first draft genome sequence of Kocuria marina SO9-6 under accession JROM00000000 (http://www.ncbi.nlm.nih.gov/nuccore/725823918), which provides insights for heavy metal bioremediation and production of compounds of biotechnological interest.
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Affiliation(s)
- Daniel B.A. Castro
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas — UNICAMP, Campinas, Brazil
| | - Letícia Bianca Pereira
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas — UNICAMP, Campinas, Brazil
| | | | - Bárbara P. da Silva
- Chemical, Biological and Agricultural Pluridisciplinary Research Center, State University of Campinas — UNICAMP, Campinas, Brazil
| | - Bruna Rafaella Z. Palermo
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas — UNICAMP, Campinas, Brazil
| | - Camila Carlos
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas — UNICAMP, Campinas, Brazil
| | - Daiane R.B. Belgini
- Chemical, Biological and Agricultural Pluridisciplinary Research Center, State University of Campinas — UNICAMP, Campinas, Brazil
| | - Elmer Erasmo G. Limache
- Chemical, Biological and Agricultural Pluridisciplinary Research Center, State University of Campinas — UNICAMP, Campinas, Brazil
| | - Gileno V. Jr Lacerda
- Chemical, Biological and Agricultural Pluridisciplinary Research Center, State University of Campinas — UNICAMP, Campinas, Brazil
| | - Mariana B.P. Nery
- Chemical, Biological and Agricultural Pluridisciplinary Research Center, State University of Campinas — UNICAMP, Campinas, Brazil
| | - Milene B. Gomes
- Chemical, Biological and Agricultural Pluridisciplinary Research Center, State University of Campinas — UNICAMP, Campinas, Brazil
| | - Salatiel S. de Souza
- Department of Animal Biology, Institute of Biology, State University of Campinas — UNICAMP, Campinas, Brazil
| | - Thiago M. da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas — UNICAMP, Campinas, Brazil
| | - Viviane D. Rodrigues
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas — UNICAMP, Campinas, Brazil
| | - Luciana C. Paulino
- Center of Natural and Human Sciences, Federal University of ABC, Santo André, Brazil
| | - Renato Vicentini
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas — UNICAMP, Campinas, Brazil
| | - Lúcio F.C. Ferraz
- Department of Molecular Biology and Pharmacology, University of São Francisco, Bragança Paulista, Brazil
| | - Laura M.M. Ottoboni
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas — UNICAMP, Campinas, Brazil
- Corresponding author. Tel.: + 551935211099.
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