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Moraes DBV, Coradine TLC, Silva EVL, Sobreira-Neto MA, Marques W, Gitaí LLG, Tumas V. Genetic Epidemiology and Clinical Characteristics of Patients with Spinocerebellar Ataxias in an Unexplored Brazilian State, Using Strategies for Resource-Limited Settings. CEREBELLUM (LONDON, ENGLAND) 2024; 23:609-619. [PMID: 37454040 DOI: 10.1007/s12311-023-01581-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/25/2023] [Indexed: 07/18/2023]
Abstract
Spinocerebellar ataxias (SCAs) have a worldwide average prevalence of 2.7 cases per 100,000 individuals, with significant geographic variability. This study aimed to develop resource-limited strategies to detect and characterize the frequency and genetic-clinical profile of SCAs in an unexplored population from Alagoas State, a low Human Development Index state in northeastern Brazil. Active search strategies were employed to identify individuals with a diagnosis or clinical suspicion of SCAs, and a protocol for clinical and molecular evaluation was applied in collaboration with a reference center in Neurogenetics. A total of 73 individuals with SCAs were identified, with a minimum estimated prevalence of 2.17 cases per 100,000 inhabitants. SCA3 was the most common type (75.3%), followed by SCA7 (15.1%), SCA1 (6.8%), and SCA2 (2.7%). Patients with SCA3 subphenotype 2 were the most predominant. Detailed analysis of patients with SCA3 and SCA7 revealed age at onset and clinical features congruent with other studies, with gait disturbance and reduced visual capacity in SCA7 as the main initial manifestations. The study also identified many asymptomatic individuals at risk of developing SCAs. These findings demonstrate that simple and collaborative strategies can enhance the detection capacity of rare diseases such as SCAs in resource-limited settings and that Alagoas State has a minimum estimated prevalence of SCAs similar to the world average.
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Affiliation(s)
- Débora Beserra Vilar Moraes
- Postgraduate Program, Department of Neurosciences and Behavioral Sciences, Ribeirão Preto Medical School, University of São Paulo, Campus Universitário - Rua Bernardino de Campos, 1000 - Centro, Ribeirão Preto, SP, 65470-000, Brazil
| | - Tácio Luis Cavalcante Coradine
- Graduation Course, Faculty of Medicine, Federal University of Alagoas, Campus Universitário, Avenida Lourival Melo Mota S/N, Tabuleiro dos Martins, CEP 57.072-900, Maceió, Alagoas, Brazil
| | - Everton Vieira Lopes Silva
- Graduation Course, Faculty of Medicine, Federal University of Alagoas, Campus Universitário, Avenida Lourival Melo Mota S/N, Tabuleiro dos Martins, CEP 57.072-900, Maceió, Alagoas, Brazil
| | - Manoel Alves Sobreira-Neto
- Division of Neurology, Faculty of Medicine, Federal University of Ceará, Rua Prof. Costa Mendes, 1408 - 4°, Andar, CEP: 60.430-140, Fortaleza, Brazil
| | - Wilson Marques
- Department of Neurosciences and Behavioral Sciences, Ribeirão Preto Medical School, University of São Paulo, Campus Universitário - Rua Bernardino de Campos, 1000 - Centro, Ribeirão Preto, SP, 65470-000, Brazil
| | - Lívia Leite Góes Gitaí
- Division of Neurology, Faculty of Medicine, Federal University of Alagoas, Campus Universitário, Avenida Lourival Melo Mota S/N, Tabuleiro dos Martins, CEP 57.072-900, Maceió, Alagoas, Brazil.
- , Maceió, Brazil.
| | - Vitor Tumas
- Department of Neurosciences and Behavioral Sciences, Ribeirão Preto Medical School, University of São Paulo, Campus Universitário - Rua Bernardino de Campos, 1000 - Centro, Ribeirão Preto, SP, 65470-000, Brazil.
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de Souza FG, Silva CS, de Araújo GS, Santana-da-Silva MN, Gobbo AR, da Silva MB, Pinto P, da Costa PF, Salgado CG, Ribeiro-Dos-Santos Â, Cavalcante GC. Mitochondrial variants of complex I genes associated with leprosy clinical subtypes. Sci Rep 2024; 14:6365. [PMID: 38493220 PMCID: PMC10944465 DOI: 10.1038/s41598-024-57191-y] [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: 10/31/2023] [Accepted: 03/15/2024] [Indexed: 03/18/2024] Open
Abstract
Leprosy is a chronic bacterial infection mainly caused by Mycobacterium leprae that primarily affects skin and peripheral nerves. Due to its ability to absorb carbon from the host cell, the bacillus became dependent on energy production, mainly through oxidative phosphorylation. In fact, variations in genes of Complex I of oxidative phosphorylation encoded by mtDNA have been associated with several diseases in humans, including bacterial infections, which are possible influencers in the host response to leprosy. Here, we investigated the presence of variants in the mtDNA genes encoding Complex I regarding leprosy, as well as the analysis of their pathogenicity in the studied cohort. We found an association of 74 mitochondrial variants with either of the polar forms, Pole T (Borderline Tuberculoid) or Pole L (Borderline Lepromatous and Lepromatous) of leprosy. Notably, six variants were exclusively found in both clinical poles of leprosy, including m.4158A>G and m.4248T>C in MT-ND1, m.13650C>A, m.13674T>C, m.12705C>T and m.13263A>G in MT-ND5, of which there are no previous reports in the global literature. Our observations reveal a substantial number of mutations among different groups of leprosy, highlighting a diverse range of consequences associated with mutations in genes across these groups. Furthermore, we suggest that the six specific variants exclusively identified in the case group could potentially play a crucial role in leprosy susceptibility and its clinical differentiation. These variants are believed to contribute to the instability and dysregulation of oxidative phosphorylation during the infection, further emphasizing their significance.
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Affiliation(s)
- Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Caio S Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Gilderlanio S de Araújo
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Mayara N Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Angélica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Moisés Batista da Silva
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Patrícia Fagundes da Costa
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Giovanna C Cavalcante
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
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de Souza FG, da Silva MB, de Araújo GS, Silva CS, Pinheiro AHG, Cáceres-Durán MÁ, Santana-da-Silva MN, Pinto P, Gobbo AR, da Costa PF, Salgado CG, Ribeiro-Dos-Santos Â, Cavalcante GC. Whole mitogenome sequencing uncovers a relation between mitochondrial heteroplasmy and leprosy severity. Hum Genomics 2023; 17:110. [PMID: 38062538 PMCID: PMC10704783 DOI: 10.1186/s40246-023-00555-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND In recent years, the mitochondria/immune system interaction has been proposed, so that variants of mitochondrial genome and levels of heteroplasmy might deregulate important metabolic processes in fighting infections, such as leprosy. METHODS We sequenced the whole mitochondrial genome to investigate variants and heteroplasmy levels, considering patients with different clinical forms of leprosy and household contacts. After sequencing, a specific pipeline was used for preparation and bioinformatics analysis to select heteroplasmic variants. RESULTS We found 116 variants in at least two of the subtypes of the case group (Borderline Tuberculoid, Borderline Lepromatous, Lepromatous), suggesting a possible clinical significance to these variants. Notably, 15 variants were exclusively found in these three clinical forms, of which five variants stand out for being missense (m.3791T > C in MT-ND1, m.5317C > A in MT-ND2, m.8545G > A in MT-ATP8, m.9044T > C in MT-ATP6 and m.15837T > C in MT-CYB). In addition, we found 26 variants shared only by leprosy poles, of which two are characterized as missense (m.4248T > C in MT-ND1 and m.8027G > A in MT-CO2). CONCLUSION We found a significant number of variants and heteroplasmy levels in the leprosy patients from our cohort, as well as six genes that may influence leprosy susceptibility, suggesting for the first time that the mitogenome might be involved with the leprosy process, distinction of clinical forms and severity. Thus, future studies are needed to help understand the genetic consequences of these variants.
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Affiliation(s)
- Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Moisés Batista da Silva
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Gilderlanio S de Araújo
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Caio S Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Andrey Henrique Gama Pinheiro
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Miguel Ángel Cáceres-Durán
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Mayara Natália Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Angélica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Patrícia Fagundes da Costa
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
| | - Giovanna C Cavalcante
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
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Sena-Dos-Santos C, Cavalcante GC, Marques D, Silva CS, de Moraes MR, Pinto P, Santana-da-Silva MN, Ferraz RS, Costa SPT, Ventura AMR, Póvoa MM, Cunha MG, Ribeiro-Dos-Santos Â. Association of apoptosis-related variants to malaria infection and parasite density in individuals from the Brazilian Amazon. Malar J 2023; 22:295. [PMID: 37794476 PMCID: PMC10552311 DOI: 10.1186/s12936-023-04729-6] [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: 02/27/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND In malaria infection, apoptosis acts as an important immunomodulatory mechanism that leads to the elimination of parasitized cells, thus reducing the parasite density and controlling immune cell populations. Here, it was investigated the association of INDEL variants in apoptotic genes-rs10562972 (FAS), rs4197 (FADD), rs3834129 and rs59308963 (CASP8), rs61079693 (CASP9), rs4647655 (CASP3), rs11269260 (BCL-2), and rs17880560 (TP53)-and the influence of genetic ancestry with susceptibility to malaria and parasite density in an admixed population from the Brazilian Amazon. METHODS Total DNA was extracted from 126 malaria patients and 101 uninfected individuals for investigation of genetic ancestries and genotypic distribution of apoptosis-related variants by Multiplex PCR. Association analyses consisted of multivariate logistic regressions, considering the following comparisons: (i) DEL/DEL genotype vs. INS/DEL + INS/INS; and (ii) INS/INS vs. INS/DEL + DEL/DEL. RESULTS Individuals infected by Plasmodium falciparum had significantly higher African ancestry proportions in comparison to uninfected controls, Plasmodium vivax, and mixed infections. The INS/INS genotype of rs3834129 (CASP8) seemed to increase the risk for P. falciparum infection (P = 0.038; OR = 1.867; 95% CI 0.736-3.725), while the DEL/DEL genotype presented a significant protective effect against infection by P. falciparum (P = 0.049; OR = 0.446; 95% CI 0.185-0.944) and mixed infection (P = 0.026; OR = 0.545; 95% CI 0.281-0.996), and was associated with lower parasite density in P. falciparum malaria (P = 0.009; OR = 0.383; 95% CI 0.113-1.295). Additionally, the INS/INS genotype of rs10562972 (FAS) was more frequent among individuals infected with P. vivax compared to P. falciparum (P = 0.036; OR = 2.493; 95% CI 1.104-4.551), and the DEL/DEL genotype of rs17880560 (TP53) was significantly more present in patients with mono-infection by P. vivax than in individuals with mixed infection (P = 0.029; OR = 0.667; 95% CI 0.211-1.669). CONCLUSIONS In conclusion, variants in apoptosis genes are associated with malaria susceptibility and parasite density, indicating the role of apoptosis-related genetic profiles in immune responses against malaria infection.
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Affiliation(s)
- Camille Sena-Dos-Santos
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Giovanna C Cavalcante
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Diego Marques
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Caio S Silva
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Milene Raiol de Moraes
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Pablo Pinto
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Dermatoimmunology, Federal University of Pará (UFPA), Marituba, Brazil
| | - Mayara Natália Santana-da-Silva
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Rafaella S Ferraz
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | | | - Ana Maria R Ventura
- Division of Parasitology, Evandro Chagas Institute (IEC), Ananindeua, Brazil
| | - Marinete M Póvoa
- Division of Parasitology, Evandro Chagas Institute (IEC), Ananindeua, Brazil
| | - Maristela G Cunha
- Laboratory of Microbiology and Immunology, Federal University of Pará (UFPA), Belém, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil.
- Program of Oncology and Medical Sciences, Oncology Research Center, Belém, Brazil.
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de Souza FG, Cavalcante GC. Mitochondria in Mycobacterium Infection: From the Immune System to Mitochondrial Haplogroups. Int J Mol Sci 2022; 23:ijms23179511. [PMID: 36076909 PMCID: PMC9455157 DOI: 10.3390/ijms23179511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
In humans, mitochondria play key roles in the regulation of cellular functions, such as the regulation of the innate immune response and are targets of several pathogenic viruses and bacteria. Mycobacteria are intracellular pathogens that infect cells important to the immune system of organisms and target mitochondria to meet their energy demands. In this review, we discuss the main mechanisms by which mitochondria regulate the innate immune response of humans to mycobacterial infection, especially those that cause tuberculosis and leprosy. Notably, the importance of mitochondrial haplogroups and ancestry studies for mycobacterial diseases is also discussed.
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Joerin-Luque IA, Augusto DG, Calonga-Solís V, de Almeida RC, Lopes CVG, Petzl-Erler ML, Beltrame MH. Uniparental markers reveal new insights on subcontinental ancestry and sex-biased admixture in Brazil. Mol Genet Genomics 2022; 297:419-435. [DOI: 10.1007/s00438-022-01857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
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Simão F, Ribeiro J, Vullo C, Catelli L, Gomes V, Xavier C, Huber G, Bodner M, Quiroz A, Ferreira AP, Carvalho EF, Parson W, Gusmão L. The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture. Genes (Basel) 2021; 12:1788. [PMID: 34828394 PMCID: PMC8625094 DOI: 10.3390/genes12111788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/25/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.
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Affiliation(s)
- Filipa Simão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Julyana Ribeiro
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team, Córdoba 14001, Argentina; (C.V.); (L.C.)
| | - Laura Catelli
- DNA Forensic Laboratory, Argentinean Forensic Anthropology Team, Córdoba 14001, Argentina; (C.V.); (L.C.)
| | - Verónica Gomes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal;
- Institute of Pathology and Molecular Immunology, University of Porto (IPATIMUP), 4099-002 Porto, Portugal
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
| | - Alfredo Quiroz
- Instituto de Previsión Social, Asunción 100153, Paraguay;
| | - Ana Paula Ferreira
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Elizeu F. Carvalho
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (G.H.); (M.B.)
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro 20550-013, Brazil; (F.S.); (J.R.); (A.P.F.); (E.F.C.)
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Ribeiro HG, Dantas-Komatsu RCS, Medeiros JFP, Carvalho MCDC, Soares VDL, Reis BZ, Luchessi AD, Silbiger VN. Previous vitamin D status and total cholesterol are associated with SARS-CoV-2 infection. Clin Chim Acta 2021; 522:8-13. [PMID: 34364853 PMCID: PMC8340549 DOI: 10.1016/j.cca.2021.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/20/2021] [Accepted: 08/03/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND The relationship of vitamin D status and other biochemical parameters with the risk of SARS-CoV-2 infection remains inconclusive, especially in regions with high solar incidence. Therefore, we aimed to associate the 25-hydroxyvitamin D (25(OH)D) concentrations and lipid profile prior to the SARS-CoV-2 tests in a population from a sunny region in Brazil (5 degrees S, 35 degrees W). METHODS This retrospective cohort study enrolled 1634 patients tested for SARS-CoV-2 of a private medical laboratory with 25(OH)D concentration and lipid profile measured ≥ 7 days before the date of the first SARS-CoV-2 RT-PCR test and were categorized according to 25(OH)D sufficiency (≥30 ng/mL) or insufficiency (<30 ng/mL). Multiple logistic regression analyses were performed to assess risk factors associated with positive tests for SARS-CoV-2. RESULTS Average serum 25(OH)D was 33.6 ng/mL. Vitamin D deficiency (<20 ng/mL) was only found in 2.6% of the participants. Multivariate analysis demonstrated that patients > 49 y with insufficient 25(OH)D (<30 ng/mL) presented increased odds to test positive for SARS-CoV-2 (OR: 2.02, 95 %CI: 1.15 to 3.55, P = 0.015). The same is observed among those with total cholesterol > 190 mg/dL (OR: 1.90, 95 %CI: 1.10 to 3.28, P = 0.020). CONCLUSIONS Previous insufficient 25(OH)D (<30 ng/mL) concentration and high total cholesterol were associated with SARS-CoV-2 infection among adults > 48 y in the study population. Further studies should be conducted to confirm whether measurement of 25(OH)D and lipid profile could be useful to identify patients who are more susceptible to COVID-19.
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Affiliation(s)
- Heriks Gomes Ribeiro
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | | | | | | | - Bruna Zavarize Reis
- Department of Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil; Postgraduate Program in Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil.
| | - André Ducati Luchessi
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, RN, Brazil; Postgraduate Program in Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Vivian Nogueira Silbiger
- Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, Natal, RN, Brazil; Postgraduate Program in Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil
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Dos Santos-Lopes SS, de Oliveira JMF, de Queiroga Nascimento D, Montenegro YHA, Leistner-Segal S, Brusius-Facchin AC, Eufrazino Gondim C, Giugliani R, de Medeiros PFV. Demographic, clinical, and ancestry characterization of a large cluster of mucopolysaccharidosis IV A in the Brazilian Northeast region. Am J Med Genet A 2021; 185:2929-2940. [PMID: 34076347 DOI: 10.1002/ajmg.a.62375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 11/08/2022]
Abstract
Mucopolysaccharidosis (MPS) IVA is a rare autosomal recessive disease with a highly variable distribution worldwide. Discrepancies in the incidence of MPS IVA among populations of different ethnicities are mostly attributed to founder effects. Demographic and clinical data from 28 MPS IVA patients, followed at a single center, and ancestry (Y chromosome and mitochondrial markers) of a subsample of 17 patients, most with the p.Ser341Arg (c.1023C>G) mutation were analyzed. Parental consanguinity was observed in 15/20 couples; a rare homozygous N-acetylgalactosamine-6-sulfatase (GALNS) mutation was found in 7/16 families with intra-familial phenotypic heterogeneity. Paternal ancestry was 94.2% (16/17) European, 5.8% (1/17) African, and 0% Amerindian. The European paternal haplogroups R1a, R1b, and R* accounted for 94.2% (16/17) of the patients. The R1b haplogroup, identified in 59% (10/17) of the patients, is frequently found in populations from the Iberian Peninsula. European, Amerindian, and African maternal ancestry was observed in 46.9% (8/17), 35.4% (6/17), and 17.7% (3/17) of the patients, respectively. Study of a cluster of MPS IVA patients from Northeastern Brazil, with high parental consanguinity and phenotypic heterogeneity showed predominantly European parental ancestry. This ancestry finding corroborates historical data on the local settlement, formed predominantly by European men.
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Affiliation(s)
| | | | | | | | - Sandra Leistner-Segal
- National Institute of Populational Medical Genetics-INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Carolina Brusius-Facchin
- National Institute of Populational Medical Genetics-INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cátia Eufrazino Gondim
- Alcides Carneiro University Hospital - HUAC, Federal University of Campina Grande, Campina Grande, Paraiba, Brazil
| | - Roberto Giugliani
- National Institute of Populational Medical Genetics-INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil.,Department of Genetics, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
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10
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Martins RB, Ordaz-Briseño SA, Flores-Hernández S, Bós ÂJG, Baptista-Rosas RC, Mercado-Sesma AR. Comparison of prevalence of diabetes complications in Brazilian and Mexican adults: a cross-sectional study. BMC Endocr Disord 2021; 21:48. [PMID: 33726717 PMCID: PMC7962221 DOI: 10.1186/s12902-021-00711-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 03/01/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Type 2 diabetes is more frequent in Latin American people than in non-Hispanic whites due to a combination of genetic and lifestyle risk factors. Brazil and Mexico are the most populous countries in Latin America. The present study aimed to compare the results of the National Health Survey "PNS" in Brazil and the National Survey Health and Nutrition "ENSANUT" in Mexico regarding the prevalence, complications and healthcare issues of diabetes in both countries. METHODS A cross-sectional study was conducted with data from the National Health Survey (PNS) of 2013 in Brazil and the National Survey of Health and Nutrition (ENSANUT) of 2018 in Mexico. The prevalence of diabetes, complications and risk factors related to developing diabetes were considered. RESULTS The respondents included 3636 individuals in Brazil and 4555 individuals in Mexico. There were significant differences in age and time living with diabetes between the two countries. Mexican people had twice as likely as Brazilian people to have a complication (p < 0.0001). The principal risk factor (OR 2.47; p ≤ 0.0001) for developing any diabetic complication was living with diabetes for more than 15 years. Visual impairment was the most frequent complication in both countries, but it was more prevalent in Mexico (p ≤ 0.001). CONCLUSIONS Diabetes complications are important health problems in Brazil and Mexico. Visual impairment was the principal complication in both countries. Several factors, such as access to and type of health system, living in a rural area, treatment, BMI and performing preventive actions, affected the risk of developing a complication. However, living with diabetes for more than 15 years was the principal risk factor. National health surveys have added significant information on the impact of diabetes in these Latin American populations. This comparison of data could provide valuable information to guide national policies and program decisions in both countries.
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Affiliation(s)
- Renata Breda Martins
- Biomedical Gerontology at Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | - Ângelo José Gonçalves Bós
- Biomedical Gerontology at Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Raúl C Baptista-Rosas
- Departamento de Salud Enfermedad como proceso individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá, Jalisco, Mexico
- Multidisciplinary Health Research Center, Centro Universitario de Tonalá/Universidad de Guadalajara (México), 45425, Tonalá, Jalisco, Mexico
| | - Arieh Roldán Mercado-Sesma
- Departamento de Salud Enfermedad como proceso individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá, Jalisco, Mexico.
- Multidisciplinary Health Research Center, Centro Universitario de Tonalá/Universidad de Guadalajara (México), 45425, Tonalá, Jalisco, Mexico.
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11
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Santos NCD, Gomes TN, Góis IADF, Oliveira JSD, Coelho LFL, Ferreira GP, Silva FRPD, Pereira ACTDC. Association of single nucleotide polymorphisms in TNF-α (-308G/A and -238G/A) to dengue: Case-control and meta-analysis study. Cytokine 2020; 134:155183. [PMID: 32731142 DOI: 10.1016/j.cyto.2020.155183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/23/2020] [Accepted: 06/15/2020] [Indexed: 01/27/2023]
Abstract
Dengue is an acute viral disease whose clinical condition is related to the interaction of factors related to the Dengue virus (DENV), environment and the host, with the immunity of the human host contributing a substantial role in the pathogenesis of DENV infection. Studies have demonstrated that single nucleotide polymorphisms (SNPs) in the promoter regions of cytokine genes such as tumor necrosis factor (TNF-α) affect transcription and/or expression; and therefore, may influence the pathogenesis of infectious diseases, such as dengue. Consequently, the objective of this study was to assess through a case-control study whether there was an association between the presence of SNPs -308G/A and -238G/A in the TNF-α gene and 158 patients with dengue and 123 controls. No association was found between the SNPs and the dengue cases in the study population. We then performed a meta-analysis, retrieving data from case-control studies in the literature for the same polymorphisms. For SNP-308G/A, the GG genotype was associated with dengue fever (DF) risk (OR = 1.24, 1.00-1.53; p = 0.05; I2 = 0%), while the GA genotype (OR = 0.75, 0.60-0.93; p = 0.01; I2 = 0%) and allele A (OR = 0.75, 0.60-0.93; p = 0.01; I2 = 0%) were associated with protection. The genotype GG population in the Asian continent (OR = 1.81 [1.06, 3.09], p = 0.03, I2 = 0%) and American (OR = 1.29 [1.00, 1.65], p = 0.05, I2 = 0%) was also associated with protection in the comparison between the cases versus the control group. In each comparison, the dominant model AA + GA (p < 0.00001) conferred protection. For SNP-238G/A the GA genotype was associated with risk for dengue hemorrhagic fever (DHF; OR = 2.17, 1.28-3.67; p = 0.004; I2 = 0%)), and the dominant AA + GA model (p < 0.00001) was associated with protection in each comparison. In summary, our results did not associate SNPs in the TNF-α gene to dengue in the Brazilian northeast population. However, combined literature data suggested the effect of the GG and GA genotypes of the SNP-308G/A on risk and protection, respectively, in Asian and American populations.
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Affiliation(s)
- Naiany Carvalho Dos Santos
- Laboratório de Biologia de Microrganismos, Universidade Federal do Delta do Parnaíba, Parnaíba, Piauí, Brazil
| | - Thiago Nobre Gomes
- Laboratório de Biologia de Microrganismos, Universidade Federal do Delta do Parnaíba, Parnaíba, Piauí, Brazil
| | - Iara Alda de Fontes Góis
- Laboratório de Biologia de Microrganismos, Universidade Federal do Delta do Parnaíba, Parnaíba, Piauí, Brazil
| | | | - Luiz Felipe Leomil Coelho
- Laboratório de Vacinas, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil
| | - Gustavo Portela Ferreira
- Laboratório de Biologia de Microrganismos, Universidade Federal do Delta do Parnaíba, Parnaíba, Piauí, Brazil
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12
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Schaan AP, Gusmão L, Jannuzzi J, Modesto A, Amador M, Marques D, Rabenhorst SH, Montenegro R, Lopes T, Yoshioka FK, Pinto G, Santos S, Costa L, Silbiger V, Ribeiro-Dos-Santos Â. New insights on intercontinental origins of paternal lineages in Northeast Brazil. BMC Evol Biol 2020; 20:15. [PMID: 31996123 PMCID: PMC6990597 DOI: 10.1186/s12862-020-1579-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022] Open
Abstract
Background The current Brazilian population is the product of centuries of admixture between intercontinental founding groups. Although previous results have revealed a heterogeneous distribution of mitochondrial lineages in the Northeast region, the most targeted by foreign settlers during the sixteenth century, little is known about the paternal ancestry of this particular population. Considering historical records have documented a series of territorial invasions in the Northeast by various European populations, we aimed to characterize the male lineages found in Brazilian individuals in order to discover to what extent these migrations have influenced the present-day gene pool. Our approach consisted of employing four hierarchical multiplex assays for the investigation of 45 unique event polymorphisms in the non-recombining portion of the Y-chromosome of 280 unrelated men from several Northeast Brazilian states. Results Primary multiplex results allowed the identification of six major haplogroups, four of which were screened for downstream SNPs and enabled the observation of 19 additional lineages. Results reveal a majority of Western European haplogroups, among which R1b-S116* was the most common (63.9%), corroborating historical records of colonizations by Iberian populations. Nonetheless, FST genetic distances show similarities between Northeast Brazil and several other European populations, indicating multiple origins of settlers. Regarding Native American ancestry, our findings confirm a strong sexual bias against such haplogroups, which represented only 2.5% of individuals, highly contrasting previous results for maternal lineages. Furthermore, we document the presence of several Middle Eastern and African haplogroups, supporting a complex historical formation of this population and highlighting its uniqueness among other Brazilian regions. Conclusions We performed a comprehensive analysis of the major Y-chromosome lineages that form the most dynamic migratory region from the Brazilian colonial period. This evidence suggests that the ongoing entry of European, Middle Eastern, and African males in the Brazilian Northeast, since at least 500 years, was significantly responsible for the present-day genetic architecture of this population.
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Affiliation(s)
- Ana Paula Schaan
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Juliana Jannuzzi
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Antonio Modesto
- Center for Oncology Research, Federal University of Pará, Belém, PA, 66073-005, Brazil
| | - Marcos Amador
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Diego Marques
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Silvia Helena Rabenhorst
- Pathology and Legal Medicine Department, Federal University of Ceará, Fortaleza, CE, 60020-181, Brazil
| | - Raquel Montenegro
- Pathology and Legal Medicine Department, Federal University of Ceará, Fortaleza, CE, 60020-181, Brazil
| | - Thayson Lopes
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - France Keiko Yoshioka
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - Giovanny Pinto
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - Sidney Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Lorenna Costa
- Clinical and Toxicological Analyses Department, Federal University of Rio Grande do Norte, Natal, RN, 59300-000, Brazil
| | - Vivian Silbiger
- Clinical and Toxicological Analyses Department, Federal University of Rio Grande do Norte, Natal, RN, 59300-000, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil. .,Center for Oncology Research, Federal University of Pará, Belém, PA, 66073-005, Brazil.
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13
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Souza AMD, Resende SS, Sousa TND, Brito CFAD. A systematic scoping review of the genetic ancestry of the Brazilian population. Genet Mol Biol 2019; 42:495-508. [PMID: 31188926 PMCID: PMC6905439 DOI: 10.1590/1678-4685-gmb-2018-0076] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 01/16/2019] [Indexed: 12/27/2022] Open
Abstract
The genetic background of the Brazilian population is mainly characterized by
three parental populations: European, African, and Native American. The aim of
this study was to overview the genetic ancestry estimates for different
Brazilian geographic regions and analyze factors involved in these estimates. In
this systematic scoping review were included 51 studies, comprehending 81
populations of 19 states from five regions of Brazil. To reduce the potential of
bias from studies with different sampling methods, we calculated the mean
genetic ancestry weighted by the number of individuals. The weighted mean
proportions of European, African, and Native American ancestries were 68.1%,
19.6%, and 11.6%, respectively. At the regional level, the highest European
contribution occurred in the South, while the highest African and Native
American contributions occurred in the Northeastern and Northern regions,
respectively. Among states in the Northeast region, Bahia and Ceará showed
significant differences, suggesting distinct demographic histories. This review
contributes for a broader understanding of the Brazilian ancestry and indicates
that the ancestry estimates are influenced by the type of molecular marker and
the sampling method.
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Affiliation(s)
- Aracele Maria de Souza
- Research Group in Molecular Biology and Immunology of Malaria, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
| | - Sarah Stela Resende
- Research Group in Molecular Biology and Immunology of Malaria, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
| | - Taís Nóbrega de Sousa
- Research Group in Molecular Biology and Immunology of Malaria, Instituto René Rachou, Fiocruz, Belo Horizonte, MG, Brazil
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14
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Whole mitochondrial genome sequencing highlights mitochondrial impact in gastric cancer. Sci Rep 2019; 9:15716. [PMID: 31673122 PMCID: PMC6823544 DOI: 10.1038/s41598-019-51951-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are organelles that perform major roles in cellular operation. Thus, alterations in mitochondrial genome (mtGenome) may lead to mitochondrial dysfunction and cellular deregulation, influencing carcinogenesis. Gastric cancer (GC) is one of the most incident and mortal types of cancer in Brazil, particularly in the Amazon region. Here, we sequenced and compared the whole mtGenome extracted from FFPE tissue samples of GC patients (tumor and internal control – IC) and cancer-free individuals (external control – EC) from this region. We found 3-fold more variants and up to 9-fold more heteroplasmic regions in tumor when compared to paired IC samples. Moreover, tumor presented more heteroplasmic variants when compared to EC, while IC and EC showed no significant difference when compared to each other. Tumor also presented substantially more variants in the following regions: MT-RNR1, MT-ND5, MT-ND4, MT-ND2, MT-DLOOP1 and MT-CO1. In addition, our haplogroup results indicate an association of Native American ancestry (particularly haplogroup C) to gastric cancer development. To the best of our knowledge, this is the first study to sequence the whole mtGenome from FFPE samples and to apply mtGenome analysis in association to GC in Brazil.
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15
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Lan Q, Xie T, Jin X, Fang Y, Mei S, Yang G, Zhu B. MtDNA polymorphism analyses in the Chinese Mongolian group: Efficiency evaluation and further matrilineal genetic structure exploration. Mol Genet Genomic Med 2019; 7:e00934. [PMID: 31478599 PMCID: PMC6785450 DOI: 10.1002/mgg3.934] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 05/26/2019] [Accepted: 07/07/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Profiling of mitochondrial DNA is surely to provide valuable investigative clues for forensic cases involving highly degraded specimens or complex maternal lineage kinship determination. But traditionally used hypervariable region sequencing of mitochondrial DNA is less frequently suggested by the forensic community for insufficient informativeness. Genome-wide sequencing of mitochondrial DNA can provide considerable amount of variant information but can be high cost at the same time. METHODS Efficiency of the 60 mitochondrial DNA polymorphic sites dispersing across the control region and coding region of mitochondrial DNA genome was evaluated with 106 Mongolians recruited from the Xinjiang Uyghur Autonomous Region, China, and allele-specific PCR technique was employed for mitochondrial DNA typing. RESULTS Altogether 58 haplotypes were observed and the haplotypic diversity, discrimination power and random match probability were calculated to be 0.981, 0.972, and 0.028, respectively. Mitochondrial DNA haplogroup affiliation exhibited an exceeding percentage (12.26%) of west Eurasian lineage (H haplogroup) in the studied Mongolian group, which needed to be further verified with more samples. Furthermore, the genetic relationships between the Xinjiang Mongolian group and the comparison populations were also investigated and the genetic affinity was discovered between the Xinjiang Mongolian group and the Xinjiang Kazak group in this study. CONCLUSION It was indicated that the panel was potentially enough to be used as a supplementary tool for forensic applications. And the matrilineal genetic structure analyses based on mitochondrial DNA variants in the Xinjiang Mongolian group could be helpful for subsequent anthropological studies.
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Affiliation(s)
- Qiong Lan
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Tong Xie
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of StomatologyXi'an Jiaotong UniversityXi'anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of StomatologyXi'an Jiaotong UniversityXi'anChina
| | - Yating Fang
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Shuyan Mei
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Guang Yang
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of StomatologyXi'an Jiaotong UniversityXi'anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of StomatologyXi'an Jiaotong UniversityXi'anChina
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16
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Sanabria DJ, Mojsiejczuk LN, Torres C, Meyer AG, Mbayed VA, Liotta DJ, Campos RH, Schurr TG, Badano I. Genetic diversity of the JC polyomavirus (JCPyV) and mitochondrial DNA ancestry in Misiones, Argentina. INFECTION GENETICS AND EVOLUTION 2019; 75:104011. [PMID: 31446138 DOI: 10.1016/j.meegid.2019.104011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/01/2019] [Accepted: 08/19/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND The use of human and viral genetic markers offers a novel way to study human migration in multiethnic populations of Latin America. OBJECTIVES Our goal was to characterize the genetic diversity and geographical origins of JC Polyomavirus (JCPyV) and the genetic ancestry of mitochondrial DNA (mtDNA) in inhabitants from 25 de Mayo, Misiones-Argentina, a small village of largely German ancestry located close to the border with Brazil. We also evaluated the extent of agreement between viral and mtDNA markers for the different ancestry components of this population. STUDY DESIGN 68 individuals were analyzed for JCPyV and mtDNA diversity. JCPyV detection and typing was conducted in urine samples by PCR amplification, sequencing and phylogenetic analysis of the VP1 gene. mtDNA ancestry was assessed through HVS1 sequencing, with the resulting haplotypes being classified into haplogroups of Amerindian, European and African origin. The distribution of JCPyV diversity and mtDNA ancestry in the population was statistically evaluated by Fisher exact test and the level of agreement of both markers at the individual level was evaluated by Cohen's kappa coefficient. RESULTS Our analysis showed that 57.4% of the samples were positive for JCPyV. Of these, the 47.6% were Asian-American Type 2, 33.3% European Type 1 and 19.1% African Type 3 in origin. The mtDNA ancestry of the study participants was 33.3% Amerindian and 66.7% European. There was a significant difference among the distribution of JCPyV diversity and mtDNA ancestry (p = 0.009) and at the individual level there was no correlation between the distribution of the both markers (κ = 0.154, p = 0.297). CONCLUSION The apparent incongruence between JCPyV diversity and mtDNA ancestry may reflect the original settlement process and more recent migration to 25 de Mayo, the latter involving viral spread through migrants from Brazil. Some potential limitations to our interpretations are also discussed.
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Affiliation(s)
- Daiana J Sanabria
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Laura N Mojsiejczuk
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Carolina Torres
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandro G Meyer
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Viviana A Mbayed
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Rodolfo H Campos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
| | - Ines Badano
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
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17
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Avila E, Graebin P, Chemale G, Freitas J, Kahmann A, Alho CS. Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods. Forensic Sci Int Genet 2019; 42:154-164. [PMID: 31325893 DOI: 10.1016/j.fsigen.2019.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022]
Abstract
The use of Massive Parallel Sequencing (MPS) techniques have been proposed by the forensic community as an alternative to Sanger sequencing methods in routine forensic casework analysis regarding mitochondrial DNA (mtDNA). Interesting features of MPS include high throughput, ability to simultaneously genotype a significant number of samples by barcoding techniques, processing automation, reduced time and costs, among others. Advantages include the capability of generating full mtDNA genome sequences versus usual techniques, usually limited to hypervariable or control regions exclusively. In this work, 96 reference single-source samples from three different Brazilian cities were subjected to full mtDNA genome sequencing by MPS techniques using an early-access version of Precision ID mtDNA Whole Genome Panel on an Ion Torrent PGM platform (Thermo Fisher Scientific, Waltham, MA, USA). Complete, high-quality sequences were obtained and sequencing performance was evaluated via four different metrics. As a subset of evaluated samples have been previously submitted for Sanger sequencing of the control region, a comparative analysis of both methods' results was conducted in order to compare technique adequacy within a forensic context. Even though this study is one of the first to report full mtDNA genome sequences for Brazilian admixed populations, the observed haplotypes exhibit a predominance of Native American and African maternal lineages in the studied sample set, reproducing results described in the literature for control regions only. Interpopulation analysis among Brazilian and 26 worldwide populations was also carried out. The results indicate that MPS-generated full mtDNA genome sequences may have great utility in forensic real casework applications, with a pronounced gain of genetic information and discrimination power provided by coding region evaluation and the enhanced capacity of heteroplasmies determination. Database construction and other relevant factors concerning implementation of such techniques in Brazilian forensic laboratories are also discussed.
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Affiliation(s)
- E Avila
- Setor Técnico-Científico, Superintendência Regional do Rio Grande do Sul, Polícia Federal, Porto Alegre, Brazil; Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil.
| | - P Graebin
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - G Chemale
- Setor Técnico-Científico, Superintendência Regional do Rio Grande do Sul, Polícia Federal, Porto Alegre, Brazil
| | - J Freitas
- Instituto Nacional de Criminalística, Polícia Federal, Brasília, DF, Brazil
| | - A Kahmann
- Instituto de Matemática, Estatística e Física, Universidade Federal de Rio Grande, Rio Grande, Brazil
| | - C S Alho
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil
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dos Reis RS, Simão F, dos Santos Stange V, Garcia FM, Spinassé Dettogni R, Stur E, da Silva AMÁ, de Carvalho EF, Gusmão L, Drumond Louro I. A view of the maternal inheritance of Espírito Santo populations: The contrast between the admixed and Pomeranian descent groups. Forensic Sci Int Genet 2019; 40:175-181. [DOI: 10.1016/j.fsigen.2019.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/22/2019] [Accepted: 03/05/2019] [Indexed: 11/28/2022]
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19
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Origin and age of the causative mutations in KLC2, IMPA1, MED25 and WNT7A unravelled through Brazilian admixed populations. Sci Rep 2018; 8:16552. [PMID: 30410084 PMCID: PMC6224410 DOI: 10.1038/s41598-018-35022-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
The mutation age and local ancestry of chromosomal segments harbouring mutations associated with autosomal recessive (AR) disorders in Brazilian admixed populations remain unknown; additionally, inbreeding levels for these affected individuals continue to be estimated based on genealogical information. Here, we calculated inbreeding levels using a runs of homozygosity approach, mutation age and local ancestry to infer the origin of each chromosomal segments containing disorder-causing mutations in KLC2, IMPA1, MED25 and WNT7A. Genotyped data were generated from 18 patients affected by AR diseases and combined to the 1000 genome project (1KGP) and Simons genome diversity project (SGDP) databases to infer local ancestry. We found a major European contribution for mutated haplotypes with recent mutation age and inbreeding values found only in Native American and Middle East individuals. These results contribute to identifying the origin of and to understanding how these diseases are maintained and spread in Brazilian and world populations.
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