Strategies for genetic study of hearing loss in the \ud Brazilian northeastern region

The overall aim of this study was to estimate the contribution of genetic factors to the etiology of hearing loss (HL) in two counties in the Brazilian northeastern region. A cross-sectional study, based on the key informant approach (KI) was conducted in Queimadas and Gado Bravo counties (Paraíba, Northeast Brazil). The sample consisted of 182 patients with HL. Genetic screening of the most frequent mutations associated with HL was performed for all samples. DFNB1 mutations were the most frequently found in both counties. The c.35delG mutation was detected in homozygosis in seven non-syndromic probands in Queimadas (7/76, 9.2%) and only a single homozygote with this mutation was found in Gado Bravo (1/44, 2.3%). We also detected the del(GJB6-D13S1854) mutation in non-syndromic probands from Gado Bravo (2/44, 4.5%). The c.189C>A (p.TyrY63*) mutation in the CLRN1 gene was detected in homozygosis in 21/23 Usher syndrome patients from Gado Bravo and it was not found in Queimadas. Cases with probable genetic etiology contributed approximately to half of HL probands in each county (54.6% in Gado Bravo and 45.7% in Queimadas). We confirm the importance of DFNB1 locus to non-syndromic HL but we show that the frequency of mutations in the northeastern region differs somewhat from those reported in southeastern Brazil and other populations. In addition, the extremely high frequency of individuals with Usher syndrome with c.189C>A variation in CLRN1 indicates the need for a specific screening of this mutation.This work was supported by CNPq, CAPES and CEPID-FAPESP. We are grateful to Dr. Ignacio del Castillo for suggestion of several protocols.We also thank the ophthalmologist Sabino Guimarães for fundoscopy of Usher syndrome patients. We thank Dr. Paulo Otto for critical reading of the manuscript. Maria Teresa Balester de Mello Auricchio for technical assistance

Position effects at the FGF8 locus are associated with femoral hypoplasia

Copy-number variations (CNVs) are a common cause of congenital limb malformations and are interpreted primarily on the basis of their effect on gene dosage. However, recent studies show that CNVs also influence the 3D genome chromatin organization. The functional interpretation of whether a phenotype is the result of gene dosage or a regulatory position effect remains challenging. Here, we report on two unrelated families with individuals affected by bilateral hypoplasia of the femoral bones, both harboring de novo duplications on chromosome 10q24.32. The ∼0.5 Mb duplications include FGF8, a key regulator of limb development and several limb enhancer elements. To functionally characterize these variants, we analyzed the local chromatin architecture in the affected individuals’ cells and re-engineered the duplications in mice by using CRISPR-Cas9 genome editing. We found that the duplications were associated with ectopic chromatin contacts and increased FGF8 expression. Transgenic mice carrying the heterozygous tandem duplication including Fgf8 exhibited proximal shortening of the limbs, resembling the human phenotype. To evaluate whether the phenotype was a result of gene dosage, we generated another transgenic mice line, carrying the duplication on one allele and a concurrent Fgf8 deletion on the other allele, as a control. Surprisingly, the same malformations were observed. Capture Hi-C experiments revealed ectopic interaction with the duplicated region and Fgf8, indicating a position effect. In summary, we show that duplications at the FGF8 locus are associated with femoral hypoplasia and that the phenotype is most likely the result of position effects altering FGF8 expression rather than gene dosage effects.M.S. and A.S.-S. were supported by the Polish National Science Centre (UMO-2016/23/N/NZ2/02362 to M.S. and UMO-2016/21/D/NZ5/00064 to A.S.-S.). A.S.-S. was also supported by the Polish National Science Centre scholarship for PhD students (UMO-2013/08/T/NZ2/00027). C.L. is supported by postdoctoral Beatriu de Pinós from Secretaria d’Universitats I Recerca del Departament d’Empresa i Coneixement de la Generalitat de Catalunya and by the Marie Sklodowska-Curie COFUND program from H2020 (2018-BP-00055). A.J. was supported by the Polish National Science Centre (UMO-2016/22/E/NZ5/00270) as well as the Polish National Centre for Research and Development (LIDER/008/431/L-4/12/NCBR/2013). M.S. is supported by grants from the Deutsche Forschungsgemeinschaft (DFG) (SP1532/3-1, SP1532/4-1, and SP1532/5-1), the Max Planck Foundation, and the Deutsches Zentrum für Luft- und Raumfahrt (DLR 01GM1925)

Epidemiologic and genetic study of deafness in two counties in the state of Paraíba, Brazil

Os estados do Nordeste brasileiro concentram elevadas taxas de pessoas com deficiências, mas pouco se estudou a respeito de suas causas. O objetivo desse estudo foi determinar a prevalência da deficiência auditiva e estimar a contribuição dos fatores genéticos na sua etiologia nas populações de dois municípios do Nordeste brasileiro. Após indicação pelos agentes comunitários de saúde para avaliação clínico-genética, foram avaliados 182 indivíduos com perda auditiva manifestada antes dos 60 anos dos municípios de Gado Bravo (76 pacientes) e Queimadas (106 pacientes), com população de 8.376 e 41.049 habitantes, respectivamente. Em Queimadas, 13 pacientes eram homozigotos com a mutação c.35delG no gene GJB2 (13/106, 12,2%; 6/81, 7,4% das famílias). Já em Gado Bravo, somente um paciente era homozigoto com esta mutação (1/76, 1,3%; 1/55, 1,8% das famílias). A mutação m.A1555G no gene mitocondrial MTRNR1 e a mutação c.167delT no gene GJB2 não foram detectadas em ambos os municípios. Quanto às deleções do GJB6, apenas a del(GJB6-D13S1854) foi encontrada em quatro casos em Gado Bravo (4/76, 5,3%; 2/55, 3,6% das famílias). Após o sequenciamento completo do gene GJB2, foi detectada a mutação p.W24X (c.G71A) em heterozigose em três casos isolados do município de Gado Bravo (3/76, 3,9%). Em resumo, mutações patogênicas no lócus DNFB1 foram encontradas em 16% (34/212) dos alelos testados no município de Queimadas e em 9,9% (15/152) dos alelos testados no município de Gado Bravo. No total da casuística, ocorreram 11 pacientes com uma única mutação recessiva detectada (monoalélica) no lócus DFNB1. As amostras desses 11 pacientes foram submetidas à análise de MLPA na tentativa de identificar uma segunda mutação, do tipo variação do número de cópias, mas nenhuma mutação foi encontrada. O gene SLC26A4 foi sequenciado em amostras de famílias com padrão de herança autossômico recessivo sem mutação detectada no lócus DFNB1, que apresentaram ligação compatível por meio de microssatélites na região próxima a esse gene. Não foi detectada nenhuma mutação patogênica na região de código desse gene. Após o estudo de ligação por meio de array de SNPs e microssatélites em uma família com quatro afetados pela síndrome de Usher do município de Gado Bravo, o gene CLRN1 apareceu como provável candidato e as amostras desses pacientes foram selecionadas para sequenciamento. Foi detectada a mutação p.Y63X em homozigose nos quatro pacientes. As amostras dos outros pacientes com essa síndrome também foram sequenciadas. Essa mutação foi encontrada em homozigose em 21 dos 23 casos de síndrome de Usher em Gado Bravo. A porcentagem de casos de surdez com provável etiologia genética em Gado Bravo e Queimadas foi estimada em 55% e 45%, respectivamenteThe states of the Brazilian Northeast concentrate high rates of people with disabilities, but little has been investigated about their causes. The aim of this study was to determine the prevalence of hearing impairment and estimate the contribution of genetic factors in its etiology in populations from two counties in the Northeast of Brazil. After indication from community health agents, 182 individuals were evaluated, presenting hearing loss before the age of 60 in the counties of Gado Bravo (76 patients) and Queimadas (106 patients), with populations of 8,376 and 41,049 inhabitants, respectively. In Queimadas, 13 homozygotes with the c.35delG mutation in the GJB2 gene were found (13/106, 12.2%, 6/81, 7.4% of probands). As for Gado Bravo (N = 76), only one patient was homozygous with this mutation (1/76, 1.3%, 1/55, 1.8% of probands). The m.A1555G mutation in the mitochondrial gene MTRNR1, and the c.167delT mutation in the GJB2 gene were not detected in both counties. As for GJB6 deletions, only the del(GJB6-D13S1854) was found in four cases from Gado Bravo (4/76, 5.3%, 2/55, 3.6% of probands). After the complete sequencing of the GJB2 gene, the p.W24X (c.G71A) mutation was detected in three isolated heterozygous cases of the Gado Bravo county (3/76, 3.9%). In two of these cases, the mutation was present along with a second recessive mutation in the DNFB1 locus. In short, pathogenic mutations in the DNFB1 locus were found in 16% (34/212) of the alleles tested in the county of Queimadas and 9.9% (15/152) of the alleles tested in the county of Gado Bravo. No pathogenic mutation was detected in the coding region of this gene. From all cases, there were 11 patients with a single recessive mutation detected (monoallelic) in DFNB1 locus. Samples of these 11 patients were analyzed for MLPA in attempt to identify a second mutation, with copy number variation, but no mutation was found. The SLC26A4 gene was sequenced in families samples with autosomal recessive hearing loss, with no mutation detected in the DFNB1 locus, presenting compatible linkage utilizing microsatellites near this gene region. After linkage study using SNPs arrays and microsatellites in a family with four affected by the Usher syndrome in Gado Bravo, the CLRN1 gene appeared as a candidate and samples of these patients were selected for sequencing. The p.Y63X mutation was detected in the homozygosis in the four individuals. Samples from other patients with this syndrome were also sequenced and this mutation was found in homozygosis 21 out of 23 cases of Usher syndrome in Gado Bravo. The percentage of cases with a probable genetic cause for hearing loss in Gado Bravo and Queimadas was estimated at 55% and 45%, respectively

Unraveling the molecular basis of SPOAN syndrome: deletion in homozygosis inregulatory region leads to KLC2 gene overexpression

A síndrome SPOAN (acrônimo do inglês spastic paraplegia, optic atrophy and neuropathy) é uma doença neurodegenerativa de herança autossômica recessiva que tem como achados clínicos a atrofia ótica congênita não progressiva, paraplegia espástica e neuropatia ambas progressivas. Ela havia sido mapeada na região cromossômica 11q13, porém a variante patogênica e o gene associados à síndrome não haviam sido identificados. Após execução do sequenciamento do genoma completo de um paciente foi detectada a deleção de 216-pb (chr11.hg19:g.66,024,557_66,024,773del) em homozigose localizada em região regulatória upstream do gene KLC2. Surpreendentemente, essa deleção causa superexpressão do KLC2, detectada em estudos de Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) utilizando fibroblastos e neurônios motores de pacientes comparados com controles. Ensaios utilizando o Danio rerio como modelo in vivo mostraram que tanto o knockdown quanto a superexpressão do klc2 em embriões de zebrafish causa o fenótipo de cauda curvada (leve ou grave); fenótipo esse associado às doenças neurodegenerativas e HSPs. Superexpressão de um gene causada por uma pequena deleção em região regulatória é um novo mecanismo que até então não havia sido descrito na condição autossômica recessiva. Estudos funcionais por meio de gene reporter de LacZ avaliando o padrão de expressão espaço-temporal da região regulatória wild-type e com a deleção de 216-pb foram realizados nesse trabalho em modelo de camundongo, porém, não foi possível identificar um padrão de expressão reprodutível do gene reporter nesse modelo. Por fim, camundongos transgênicos para a superexpresão do KLC2 humano foram gerados, no entanto não foram realizados testes físicos e comportamentais para validar o transgênico como modelo para síndrome SPOANSPOAN (the acronym of its clinical symptoms) syndrome is a neurodegenerative disorder mainly characterized by a progressive spastic paraplegia, congenital non-progressive optic atrophy and progressive neuropathy. A potential causative gene was mapped at 11q13, but so far no gene and mutation were identified. Whole-genome sequencing allowed to detect a homozygous 216-bp deletion (chr11.hg19:g.66,024,557_66,024,773del) located at the regulatory upstream region of the KLC2 gene. Surprisingly, this deletion causes KLC2 overexpression detected by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) using fibroblasts and motor-neurons from patients compared with controls. Assays using Danio rerio as in vivo model showed that the klc2 knockdown either its overexpression in zebrafish embryos causes mild to severe curly-tail phenotype; phenotype that is already well defined as suggestive of a neurodegenerative disorder and HSP. Overexpression of a gene caused by a small deletion in the regulatory region is a novel mechanism, which to the best of our knowledge, was never reported before in a recessive condition. Functional studies using LacZ reporter assay evaluating the spatiotemporal expression pattern of wild-type regulatory region and with the deletion of 216-bp were performed in this work using mouse, but was not possible to identify an especific gene reporter expression pattern in this animal model. As a last experiment, transgenic mice for human KLC2 overexpression were generated, though behavioral tests were not performed to validate this transgenic animal as a model for SPOAN syndrom

Origin and age of the causative mutations in KLC2, IMPA1, MED25 and WNT7A unravelled through Brazilian admixed populations

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