Amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) are the commonest motor neuron diseases of adult- and childhood onset. Alterations of the RNA binding protein TDP-43 are associated with most cases of ALS, while SMA is caused by deletion of the Survival Motor Neuron (SMN1) gene. SMN has been well characterised in its role in the assembly of the cellular machinery that carries out splicing of pre-mRNA, but is thought to have other functions in RNA metabolism unrelated to pre-mRNA splicing. It is conceivable that specific aspects of RNA handling are disrupted in both SMA and ALS. A variety of genetic, molecular and neuropathological approaches were applied to investigate a potential common pathway in these diseases. The spectrum of genetic mutations underlying motor neuron disorders were explored by screening patient DNA. Cell culture and mouse models were used to test the hypothesis that altered pre-mRNA splicing causes motor neuron death. Human neuropathological specimens were examined for changes in proteins involved in RNA metabolism. The results indicate that altered pre-mRNA splicing is a late occurrence in disease and more likely to be a consequence rather than the cause of motor neuron degeneration. However, the notion that RNA metabolism is highly relevant to motor neuron diseases was strengthened by the discovery of mutations in another RNA binding protein, FUS, in cases of ALS without TDP-43 pathology. Overall the findings highlight the need to consider disruption of mRNA transport and regulation of mRNA translation in future motor neuron disease research.

Humans display a 90% population level bias towards right-handedness, implying the vast majority of people have a left-hemisphere dominant for motor control. Although handedness presents a weak, but very consistent heritability across the literature (estimated to be approximately 25%), to date few genetic loci associated with this complex trait have been identified and replicated in subsequent studies. One such gene which has been found to be associated with handedness and subsequently replicated is PCSK6, most recently through a quantitative GWAS (P < 0.5*10−8, Brandler et al. (2013)). Interestingly, PCSK6 is known to activate Nodal, a morphogen involved in a highly conserved bilaterian pathway known to regulate left-right body axis determination. Here I present the first molecular characterisation of a handedness-associated region by conducting a detailed functional analysis of the PCSK6 locus, combining genetic analysis, in silico prediction and molecular assays to investigate how common genetic variants influence handedness-related phenotypes. Specifically, I defined the associated locus to be 12.7 kb in size, spanning a predicted 1.8 kb bidirectional promoter which controls the expression of both an antisense long non-coding RNA (lncRNA), and a novel short PCSK6 isoform. A series of luciferase-expressing constructs were generated to characterise the promoter, identifying a minimal sequence capable of driving transcription in a sense strand direction. I have demonstrated experimentally that one of the top associated markers in previous GWA studies, rs11855145, directly creates/disrupts a suspected transcription factor bind site in the vicinity of this bidirectional promoter. Further functional studies of the genetic variation within PCSK6 may help explain the molecular regulatory mechanisms affecting gene expression. This project provides a model for assays to study other GWAS-nominated candidate genes, and in particular for establishing the role of noncoding variants. The findings from this study support the role of common variants in influencing complex phenotypes, such as handedness.

Alzheimer's disease (AD) is the most common neurodegenerative disease, characterized by progressive amyloid plaque aggregation, neurofibrillary tangles, and cortical tissue death. As the prevalence of AD is projected to climb in coming years, there is a vested interest in identifying endophenotypes by which to improve diagnostics and direct clinical interventions. The risk for complex disorders, such as AD, is influenced by multiple genetic, environmental, and lifestyle factors. Significant strides have been made in identifying genetic variants linked to AD through the genome-wide association study (GWAS). It has been estimated in more recent years, however, that GWAS-identified variants account for limited AD heritability, suggesting the role of non-sequence genetic mechanisms, such as epigenetic moderators. By influencing gene expression, epigenetic markers have been linked to age- associated decline through modulation of chromatin architecture and global genome instability, though such mechanisms are also involved with a number of normal biological processes, including neurogenesis. As the strategies of clinical genetics shift to include a heavier focus on epigenetic contributors, altered adult neurogenesis presents itself as a strong candidate for an endophenotype of AD development. This thesis proposes that, due to neuropathological dysfunction of epigenetic mechanisms in AD, new generations of neurons fail to proliferate, differentiate, and mature correctly, resulting in the larger loss of neurons and cognitive deficits characteristic to neurodegenerative disease. The plasticity of the epigenome and the role of epigenetic factors as mediators of the genome and the environment make such alterations attractive in AD research and implies the potential for therapeutic interventions. The present review submits neurogenesis as a viable target of epigenetic research in AD, highlights shared loci between neurogenesis and AD in the epigenome, and considers the promises and limitations of the neurogenic endophenotype.

It is now well accepted, through the use of mutational studies, that genes influence behavioural variation. However, we have little knowledge of the cellular and neuronal mechanisms underlying the effects of specific genes. This thesis broadens our understanding of the neurogenetic underpinnings of naturally occurring differences in behaviour using the genetically tractable model organism Drosophila melanogaster. The thesis focuses on allelic variation at the foraging (for) gene which influences both larval and adult behaviour. In particular, for’s cellular/neural contributions to food-related behaviours and learning and memory is investigated. In the first study, we map FOR protein distribution patterns in the adult brain and use this knowledge to demonstrate a neural-specific function for the for gene in adult food-related behaviour. In the second study we demonstrate a novel role for for in the regulation of naturally existing differences in fly learning and memory in the mushroom bodies of the fly brain. In the third study, I explore FOR distribution patterns in larval tissues. I show that FOR is expressed both in neural and non-neural tissues suggesting a distributed function for FOR in food-related behaviours in the larva. In the last study, I describe naturally existing differences in fat metabolism in the Drosophila larva fat storage tissue. FOR is expressed in the fat storage tissue and may regulate lipid packaging, a trait linked to foraging. In general, my thesis is a cellular and neurogenetic analysis of natural variation in behavioural and physiological traits of D. melanogaster. The functions of FOR in food-related behaviours, nutrient physiology and cognition are conserved across taxa. The findings of this thesis should provide a framework to understand these phenomena in a wide range of organisms.

It is now well accepted, through the use of mutational studies, that genes influence behavioural variation. However, we have little knowledge of the cellular and neuronal mechanisms underlying the effects of specific genes. This thesis broadens our understanding of the neurogenetic underpinnings of naturally occurring differences in behaviour using the genetically tractable model organism Drosophila melanogaster. The thesis focuses on allelic variation at the foraging (for) gene which influences both larval and adult behaviour. In particular, for’s cellular/neural contributions to food-related behaviours and learning and memory is investigated. In the first study, we map FOR protein distribution patterns in the adult brain and use this knowledge to demonstrate a neural-specific function for the for gene in adult food-related behaviour. In the second study we demonstrate a novel role for for in the regulation of naturally existing differences in fly learning and memory in the mushroom bodies of the fly brain. In the third study, I explore FOR distribution patterns in larval tissues. I show that FOR is expressed both in neural and non-neural tissues suggesting a distributed function for FOR in food-related behaviours in the larva. In the last study, I describe naturally existing differences in fat metabolism in the Drosophila larva fat storage tissue. FOR is expressed in the fat storage tissue and may regulate lipid packaging, a trait linked to foraging. In general, my thesis is a cellular and neurogenetic analysis of natural variation in behavioural and physiological traits of D. melanogaster. The functions of FOR in food-related behaviours, nutrient physiology and cognition are conserved across taxa. The findings of this thesis should provide a framework to understand these phenomena in a wide range of organisms.

Thesis (M. Phil.)--University of Hong Kong, 2005. / Title proper from title frame. Also available in printed format.

Orientador: Iscia Teresinha Lopes Cendes / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-23T06:36:18Z (GMT). No. of bitstreams: 1 Gonsales_MarinaCoelho_D.pdf: 5961380 bytes, checksum: 501b9df1659eb15a6a8545ae0943d967 (MD5) Previous issue date: 2013 / Resumo: As epilepsias são distúrbios cerebrais caracterizados por uma predisposição persistente para a geração de crises epilépticas, que são interrupções transitórias no funcionamento normal do sistema nervoso. Acredita-se que a maioria das epilepsias relacionadas com idade de inicio precoce possui etiologia presumivelmente genética. Sendo assim, elas representam um grupo para o qual o uso de testes genéticos seria potencialmente benéfico. Os objetivos principais deste trabalho foram: a caracterização das bases moleculares de diferentes formas de epilepsia da infância e da adolescência e a avaliação do potencial dos genes candidatos estudados para a utilização em testes genéticos para fins clínicos. A estratégia empregada foi à triagem de mutações nos seguintes genes: SCN1A, em pacientes com síndromes de Dravet e de Doose; SCL2A1 em pacientes com síndrome de Doose e epilepsias idiopáticas generalizadas (EIGs), especialmente a epilepsia mioclonica juvenil (EMJ); e EFHC1 e GABRA1, em pacientes com EMJ e outras formas comuns de EIGs. A triagem de mutações foi realizada por sequenciamento automático pela técnica de Sanger. As alterações potencialmente deletérias foram investigadas em um grupo controle composto por 100 indivíduos sem epilepsia. O potencial deletério das substituições que resultam em troca do resíduo de aminoácido na proteína codificada foi estimado utilizando-se diferentes algoritmos de predição. As mutações previamente descritas na literatura foram compiladas e analisadas quanto a sua provável localização na proteína e predição de efeito deletério. Analises por Multiplex Ligation-dependent Probe Amplification (MLPA) foram realizadas para a detecção de variações no numero de copias de SCN1A. A analise de mutações no gene SCN1A revelou alterações potencialmente deletérias em 81% dos pacientes com síndrome de Dravet, e em apenas um paciente com síndrome de Doose. Esses dados, juntamente com os resultados das analises de compilação das mutações descritas na literatura, sugerem que o teste genético em SCN1A para fins clínicos seria altamente recomendável em indivíduos com síndrome de Dravet, mas não para os com síndrome de Doose típica. O gene SLC21A não parece estar envolvido na etiologia da síndrome de Doose e das EIGs em nossa casuística. A frequencia de alterações potencialmente deletérias no gene EFHC1 em indivíduos com EMJ foi relativamente baixa, sugerindo que esse gene não seja o principal causador dessa epilepsia, embora possa ser um fator de predisposição. Por fim, o gene GABRA1 não parece conferir predisposição para as EIGs comuns em nossa casuística / Abstract: Epilepsy is a brain disorder characterized by a long lasting predisposition to generate epileptic seizures, which are transient interruptions of normal brain function. Most epilepsies with early onset presumably have a genetic etiology. Thus, they represent a group for which the use of genetic testing would be potentially beneficial. The main goals of this study were to characterize the molecular basis of different forms of epilepsy in childhood and adolescence and to evaluate the potential clinical use of genetic testing in the context of these disorders. To achieve these goals we searched for mutations in the following genes: SCN1A in patients with Dravet and Doose syndromes; SLC2A1 in patients with Doose syndrome and idiopathic generalized epilepsies (IGEs), particularly juvenile myoclonic epilepsy (JME); and EFHC1 and GABRA1 in patients with JME and other common forms of IGEs. Mutation screening was performed by automated Sanger sequencing using capillary electrophoresis. Potentially deleterious nucleotide changes found were subsequently investigated in a control group of 100 individuals without epilepsy. In addition, the deleterious potential of amino acid changes identified was estimated using different prediction algorithms. Mutations previously described in the literature were compiled and analyzed regarding their putative location on the protein and predicted deleterious effect. Furthermore, Multiplex Ligation-dependent Probe Amplification (MLPA) analyzes were performed to detect the presence of copy number variations in SCN1A. Our results showed potentially deleterious variants in SCN1A in 81% of patients with Dravet syndrome, but only in one patient with Doose syndrome. These data, along with the results of the compilation of mutations reported in the literature suggest that genetic testing for SCN1A is clinically relevant in Dravet syndrome, but not in typical Doose syndrome. SLC21A does not seem to be involved in the etiology of Doose syndrome and EIGs in our cohort. The frequency of potentially deleterious changes in EFHC1 in individuals with JME was relatively low, suggesting that this gene is not the main cause of this form of epilepsy, although it may be a predisposing factor. Lastly, GABRA1 does not seem to confer predisposition to common EIGs in our cohort / Doutorado / Fisiopatologia Médica / Doutora em Ciências

No description available.

<p>Down syndrome (DS) is a genetic condition caused by the triplication of human chromosome  21 and presents with many phenotypes including decreased brain size, hypocellularity in the brain,  and assorted ocular phenotypes. Some of the ocular phenotypes seen are increased risk of cataracts,  accommodation difficulties, increased risk of refractive errors, and increased retinal thickness. The  Ts65Dn mouse model of DS is a classically used mouse model as it presents a number of  phenotypes also seen in those with DS. Some of these phenotypes include decreased brain volume,  abnormal synaptic plasticity, and ocular phenotypes. These ocular phenotypes include decreased  visual acuity, cataracts, and increased retinal thickness. The Ts65Dn mouse model is trisomic for <em>Dyrk1a</em>, a gene of interest in DS research. We hypothesize that there will be a genotypic and sex effect of retinal thickness and retinal ganglion cell (RGC) count at postnatal day 15 in the Ts65Dn  mouse model of DS. Retinal slices were taken from male and female trisomic and euploid Ts65Dn  mice at P15 and fluorescently labeled for RGCs and bipolar cells via immunohistochemistry. The  retinas were measured for total retinal thickness and RNA-binding protein (RBPMS) positive cells in the RGC layer were counted. There was no genotypic or sex effect when comparing retinal  thickness in trisomic mice as compared to euploid mice. There was a genotypic effect of RBPMS  positive cell count in which the trisomic mice had a higher number of RBPMS positive cells than  euploid mice. Increased retinal thickness along with increased RGC number have both been  implicated with decreased apoptosis in the retina. In the Ts65Dn mouse model along with in  individuals with DS, this could be due to an increase in DYRK1A protein levels reducing apoptosis.  In future studies, determining DYRK1A’s influence in retinal thickness and RGC number could  result in a treatment for overactive <em>DYRK1A</em> that could normalize retinal thickness and RGC  number in those with DS.</p>

<p dir="ltr">Genome-wide association studies (GWAS) have uncovered numerous variants linked to a wide range of complex traits. However, understanding the mechanisms underlying these associations remains a challenge. To determine genetically regulated mechanisms, additional layers of gene regulation, such as transcriptome and proteome, need to be assayed. Transcriptome-wide association studies (TWAS) and Proteome-wide association studies (PWAS) offer a gene-centered approach to illuminate these mechanisms by examining how variants influence transcript expression and protein expression, thereby inferring their impact on complex traits. In the introductory chapter of this dissertation, I discuss the methodology of TWAS and PWAS, exploring the assumptions they make in estimating SNP-gene effect sizes, their applications, and their limitations. In Chapter 2, I undertake an integrative analysis of TWAS and PWAS using the largest cohort of individuals affected with Tourette’s Syndrome within the Psychiatric Genomics Consortium (PGC) – Tourette’s Syndrome working group. I identified genomic regions containing multiple TWAS and PWAS signals and integrated these results using the computational colocalization method to gain insights into genetically regulated genes implicated in the disorder. In Chapter 3, I conduct an extensive TWAS of the Myasthenia Gravis phenotype, uncovering novel genes associated with the disorder. Utilizing two distinct methodologies, I performed individual tissue-based and cross-tissue-based imputation to assess the genetic influence on transcript expression. A secondary TWAS analysis was conducted after removing SNPs from the major histocompatibility complex (MHC) region to identify significant genes outside this region. Finally, in Chapter 4, I present the conclusions drawn from both studies, offering a comprehensive understanding of the genetic architecture underlying these traits. I also discuss future directions aimed at advancing the mechanistic understanding of complex non-Mendelian disorders.</p>