Submitted by Leonardo Cavalcante (leo.ocavalcante@gmail.com) on 2018-04-23T22:50:06Z No. of bitstreams: 1 Arquivototal.pdf: 7015058 bytes, checksum: 0d8c1dd0bc2f42ab36a2d917f1dc6a05 (MD5) / Made available in DSpace on 2018-04-23T22:50:06Z (GMT). No. of bitstreams: 1 Arquivototal.pdf: 7015058 bytes, checksum: 0d8c1dd0bc2f42ab36a2d917f1dc6a05 (MD5) Previous issue date: 2015-07-06 / A part of the populations in Northeastern Brazil are relatively isolated geographically and these populations maintain the tradition of consanguineous marriages for generations. These two factors (isolation and inbreeding) increase the risk of birth of people with autosomal recessive intellectual disabilities. The objective of this study was to determine the genetic causes of intellectual disabilities in two large consanguineous families of Paraiba backlands. In 2012, we conducted an epidemiological study to investigate the contribution of genetic factors in determining the deficiencies in six municipalities of Paraíba previously selected by presenting high consanguinity rate. Families who had patients with neurodegenerative disorders and/or intellectual disabilities (ID) were invited by community health agents for a first screening realized by biologists in order to select patients with deficiency probably caused by genetic mutations. In total, 276 patients were screened, of which, 109 were selected for medical evaluation with neurologists. After medical evaluation, two families with multiple affected individuals in two different forms of autosomal recessive intellectual disability were selected for clinical and genetic research. We performed the linkage study using SNPs array analysis to determine homozygous regions. Subsequently, the whole exome sequencing (WES) of one affected individual of each family was sequenciated. Potentially deleterious variants detected in regions of homozigosity-by descent which were not present in Brazilian population controls or in exomes of global online databases were subject to further scrutiny and segregation analysis by Sanger sequencing. Family A has seven adult siblings with syndromic ID. Phenotype includes tall forehead, prognatism, prominent chin, very large and overhanging nose tip. Homozigosity-by-descent analysis found a 4.0 Mb region in 19q13.32-q13.33 (lod score: 3.24). WES disclosed a homozygous variant (c.418C>T, p.Arg140Trp) in mediator complex subunit 25 (MED25), predicted as deleterious by Provean, Mutation Taster, PolyPhen-2 and SIFT. MED25 is a component of the Mediator complex, involved in regulation of transcription of nearly all RNA polymerase II-dependent genes. Deleterious mutations in MED12, MED17, MED23 and recently after our publication another mutation in the MED25 have been associated with ID. Family B has nine affected adults descending from four closely related first-cousin couples affected by severe non-syndromic ID. Homozigosity-by-descent analysis disclosed a 20.7 Mb region in 8q12.3-q21.2 (lod score: 3.11). WES identified a homozygous deleterious variant in inositol monophosphatase1 gene (IMPA1), consisting of a 5 bp duplication (c.489_493dupGGGCT) leading to frameshift (p.Ser165Trpfs*10). IMPA1 gene product is responsible for the final step of biotransformation of inositol triphosphate and diacylglycerol, two second messengers, and up to now, despite its many physiological functions, no clinical phenotype has been assigned to this gene dysfunction. From this study, it was possible to develop diagnostic test by restriction enzyme and therapeutic perspective for cases associated with IMPA1. / Uma parte das populações do Nordeste brasileiro está relativamente isolada geograficamente e mantêm, há várias gerações, a tradição de casamentos consanguíneos. Esses dois fatores associados (isolamento e endocruzamento) elevam o risco de nascimento de pessoas com deficiência intelectual com herança genética autossômica recessiva. O objetivo deste trabalho foi determinar as causas genéticas da deficiência intelectual em duas grandes famílias consanguíneas do sertão paraibano. Em 2012, nosso grupo de pesquisa realizou um estudo epidemiológico para determinar a contribuição de fatores genéticos na determinação das deficiências em seis municípios do sertão paraibano selecionados previamente por apresentarem elevada taxa de consanguinidade. As famílias que apresentavam repetições de indivíduos com doenças neurodegenerativas e/ou deficiência intelectual (DI) foram convocadas pelos agentes comunitários de saúde para uma primeira triagem, realizada pelos biólogos geneticistas, a fim de selecionar pacientes que apresentavam deficiência por prováveis causas genéticas. No total, foram triados 276 pacientes, sendo que, 109 foram selecionados para avaliação médica com neurologistas. Após a avaliação médica, duas famílias com múltiplos indivíduos acometidos por duas diferentes formas de DI de herança autossômica recessiva foram selecionadas para investigação clínico-genética. O estudo de ligação para determinar regiões em homozigose foi realizado com o uso da técnica de array de SNPs. Posteriormente, foi feito o sequenciamento do exoma completo de um indivíduo afetado de cada família. Variantes potencialmente deletérias detectadas em regiões em homozigose e que não estavam presentes em controles brasileiros e em banco de dados mundiais, foram objetos de uma análise mais aprofundada e feito a análise de co-segregação através do sequenciamento de Sanger. A primeira família estudada, a família A, possui sete adultos com DI sindrômica. O fenótipo inclui testa alta, prognatismo, queixo proeminente e ponta do nariz saliente, além da DI grave. O estudo de ligação apontou duas regiões com LOD scores máximos = 3,234, uma região de 26 Mb no cromossomo 2 (2p12 - q11.2) e uma região de 4,0 Mb no cromossomo 19 (19q13.32 - q13.33). O sequenciamento do exoma revelou uma variante em homozigose (c.418C>T, p.Arg140Trp) no gene MED25 (subunidade 25 do complexo mediador), predita como deletéria por diferentes softwares (Polyphen, Provean, Mutation Taster e SIFT). O complexo mediador está envolvido na regulação da transcrição de quase todos os genes dependentes da RNA polimerase II. Mutações deletérias nos genes MED12, MED17, MED23 e, recentemente, outra mutação no MED25, têm sido associadas com DI. Já a segunda família estudada, a família B, possui nove adultos afetados, descendentes de quatro relações consanguíneas entre primos de primeiro grau, com DI grave não-sindrômica. O estudo de ligação apontou uma região de 20,7 Mb no cromossomo 8 (8q12.3-q21.2) com LOD score = 3,11. O sequenciamento do exoma identificou uma variante deletéria em homozigose no gene inositol monofosfatase1 (IMPA1), que consiste em uma duplicação de 5 pares de bases (c.489_483dupGGGCT), levando a uma mutação do tipo frameshift (p.Ser165Trpfs*10). O produto do gene IMPA1 é uma enzima responsável pela etapa final da biotransformação dos segundos mensageiros inositol trifosfato e diacilglicerol, e até o momento, apesar de apresentar importantes funções fisiológicas, não havia fenótipo clínico atribuído a esse gene. A partir deste estudo, foi possível desenvolver teste diagnóstico com triagem por enzima de restrição e perspectiva de tratamento terapêutico para os casos associados ao IMPA1.

Proteins function as worker molecules in the cell and their natural environment is crowded. How they fold in a cell-like environment and how they recognize their interacting partners in such conditions, are questions that underlie the work of this thesis. Two distinct subjects were investigated using a combination of biochemical- and biophysical methods. First, the unfolding/dissociation of a heptameric protein (cpn10) in the presence of the crowding agent Ficoll 70. Ficoll 70 was used to mimic the crowded environment in the cell and it has been used previously to study macromolecular crowding effects, or excluded volume effects, in protein folding studies. Second, the conformational changes upon interaction between the Mediator subunit Med25 and the transcription factor Dreb2a from Arabidopsis thaliana. Mediator is a transcriptional co-regulator complex which is conserved from yeast to humans. The molecular mechanisms of its action are however not entirely understood. It has been proposed that the Mediator complex conveys regulatory signals from promoter-bound transcription factors (activators/repressors) to the RNA polymerase II machinery through conformational rearrangements. The results from the folding study showed that cpn10 was stabilized in the presence of Ficoll 70 during thermal- and chemical induced unfolding (GuHCl). The thermal transition midpoint increased by 4°C, and the chemical midpoint by 0.5 M GuHCl as compared to buffer conditions. Also the heptamer-monomer dissociation was affected in the presence of Ficoll 70, the transition midpoint was lower in Ficoll 70 (3.1 μM) compared to in buffer (8.1 μM) thus indicating tighter binding in crowded conditions. The coupled unfolding/dissociation free energy for the heptamer increased by about 36 kJ/mol in Ficoll. Altogether, the results revealed that the stability effect on cpn10 due to macromolecular crowding was larger in the individual monomers (33%) than at the monomer-monomer interfaces (8%). The results from the interaction study indicated conformational changes upon interaction between the A. thaliana Med25 ACtivator Interaction Domain (ACID) and Dreb2a. Structural changes were probed to originate from unstructured Dreb2a and not from the Med25-ACID. Human Med25-ACID was also found to interact with the plant-specific Dreb2a, even though the ACIDs from human and A. thaliana share low sequence homology. Moreover, the human Med25-interacting transcription factor VP16 was found to interact with A. thaliana Med25. Finally, NMR, ITC and pull-down experiments showed that the unrelated transcription factors Dreb2a and VP16 interact with overlapping regions in the ACIDs of A. thaliana and human Med25. The results presented in this thesis contribute to previous reports in two different aspects. Firstly, they lend support to the findings that the intracellular environment affects the biophysical properties of proteins. It will therefore be important to continue comparing results between in vitro and cell-like conditions to measure the magnitude of such effects and to improve the understanding of protein folding and thereby misfolding of proteins in cells. Better knowledge of protein misfolding mechanisms is critical since they are associated to several neurodegenerative diseases such as Alzheimer’s and Parkinson's. Secondly, our results substantiate the notion that transcription factors are able to bind multiple targets and that they gain structure upon binding. They also show that subunits of the conserved Mediator complex, despite low sequence homologies, retain a conserved structure and function when comparing evolutionary diverged species.

A idade da mutação e a ancestralidade local de segmentos cromossômicos que contém mutações associadas a doenças autossômicas recessivas em populações miscigenadas brasileiras continuam desconhecidas. Adicionalmente, a determinação dos níveis de endogamia continua grosseiramente estimados por abordagem genealógica e nada se sabe sobre a linhagem materna das famílias com indivíduos com doenças autossômicas recessivas. A tese está dividida em dois estudos. O primeiro visou calcular os níveis de endogamia pela abordagem de grandes regiões em homozigose, estimar a idade da mutação e inferir a ancestralidade local para determinar a origem de cada segmento cromossômico contendo mutações em KLC2, IMPA1, MED25 e WNT7A. Foram genotipadas amostras de 19 pacientes com doenças autossômicas recessivas. Os dados genotipados passaram por distintos procedimentos de filtragem para estimar os níveis de endocruzamento por abordagem molecular, para calcular a idade das mutações por meio de haplótipos, para inferir a ancestralidade global utilizando ADMIXTURE e Análise de Componentes Principais, e de forma refinada foi inferida a ancestralidade local pelo software RFMix combinando os dados de nossas amostras com os dados do projeto 1000 genomas (one thousand genome project - 1KGP) e projeto de diversidade genômica Simons (Simons genomic diversity project - SGDP). Os resultados apresentados não diferiram bastante do esperado para populações endogâmicas e miscigenadas do nordeste brasileiro de acordo com a literatura. A mutação em KLC2 mostrou-se mais antiga em relação às demais. Em um segundo estudo, para os indivíduos com mutação em KLC2 prosseguimos com a inferência dos haplogrupos de DNA mitocondrial para determinar a origem da linhagem materna das famílias. Onze pacientes com mutação em KLC2 foram escolhidos para sequenciamento de Sanger da região controle do DNA mitocondrial para determinação da matrilinhagem. Foi encontrado um possível haplogrupo fundador que pode corroborar narrativas históricas de entrada de mães sefarditas no litoral do Nordeste junto com os holandeses. Ambos trabalhos apresentam como novidade a contribuição para identificar a origem e entender como essas doenças são mantidas e dispersas em populações do Brasil e do mundo. Em especial, a matrilinhagem exibiu evidências de ligação entre as mães de famílias com indivíduos com mutação em KLC2 e mães de judeus sefarditas portugueses / 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 roughly estimated by genealogical approach, and the maternal lineage of the families with affected individuals is unknown. The thesis is divided into two studies. The first one aimed to calculate inbreeding levels by runs of homozygosity approach, estimating the age of the mutation and inferring the local ancestry to determine the origin of each chromosomal segment containing mutations in KLC2, IMPA1, MED25 e WNT7A. Samples from 19 patients with autosomal recessive diseases were genotyped. The genotyped data underwent different filtering procedures to estimate the inbreeding levels by molecular approach, to calculate the age of the mutations by means of haplotypes, to infer the global ancestry using ADMIXTURE and Principal Component Analysis, and to infer refined the local ancestry by the RFMix software combining the data from our samples with the one thousand genome project (1KGP) and the Simons genomic diversity project (SGDP). The results presented did not differ significantly from those expected for inbred and admixed populations of the Brazil Northeast according to the literature. The mutation in KLC2 was older in relation to the others. In a second study, for individuals with a KLC2 mutation, we proceeded with the inference of mitochondrial DNA haplogroups to determine the origin of the families\' maternal lineage. Eleven patients with mutation in KLC2 were chosen for Sanger sequencing of the mitochondrial DNA control region for determination of matrilineage. It was found a possible founding haplogroup that can corroborate historical narratives of Sephardic mothers\' influx along the coast of the Northeast with the Dutch. Both papers present as a novelty the identification of the origin and the understanding of how these diseases are maintained and dispersed in populations of Brazil and the world. In particular, the matrilineage exhibited an evidence of kinship among mothers of families with individuals with mutation in KLC2 and mothers of portuguese Sephardic jews