Long-lived individuals of the opportunistic fungal pathogen Armillaria gallica arise in single mating events, and then grow vegetatively to occupy large territories including multiple woody substrates. In effect, this leaves a spatial record of mutation, the detection of which would allow new inferences about how fungal individuals grow and infect their hosts. In this thesis, I first identified a large individual of A. gallica in eastern Ontario. I then searched for genetic variation within this individual by focusing on the tandemly repeated rRNA gene cluster and four microsatellite markers that are variable in the A. gallica population. I discovered a loss of heterozygosity (LOH) in the rRNA gene-cluster region, forming two genotypes that show significant spatial clustering in a Mantel test. My M.Sc. thesis research serves as a baseline for a genome-wide study of the mutational dynamic within the vegetative growth phase of this large and old Armillaria individual.

Long-lived individuals of the opportunistic fungal pathogen Armillaria gallica arise in single mating events, and then grow vegetatively to occupy large territories including multiple woody substrates. In effect, this leaves a spatial record of mutation, the detection of which would allow new inferences about how fungal individuals grow and infect their hosts. In this thesis, I first identified a large individual of A. gallica in eastern Ontario. I then searched for genetic variation within this individual by focusing on the tandemly repeated rRNA gene cluster and four microsatellite markers that are variable in the A. gallica population. I discovered a loss of heterozygosity (LOH) in the rRNA gene-cluster region, forming two genotypes that show significant spatial clustering in a Mantel test. My M.Sc. thesis research serves as a baseline for a genome-wide study of the mutational dynamic within the vegetative growth phase of this large and old Armillaria individual.

A major unanswered question in neuroscience is whether there exists genomic variability between individual neurons of the brain, contributing to functional diversity or to an unexplained burden of neurologic disease. To address this question, we developed methods to amplify genomes of single neurons from human brains, achieving >80% genome coverage of single-cells and allowing study of a wide-range of somatic mutation types.

Cancer is a devastating condition, yet its prevalence is not surprising when one considers the possibility that growth and motility define the default state of epithelial cells. What is more surprising is that epithelial cells can be induced to a “fragile quiescent state” in multicellular organisms through constant inhibitory influences from extracellular sources. In other words, the immotile and growth-constrained behavior we associate with epithelia (quiescence) is not the default state cells in a multicellular organism, but rather must be exogenously induced by tissue-specific (and systemic) factors. Quiescence therefore, is a fragile existence for any cell, as the removal of differentiating signals should cause the cell to revert to a migratory, stem-like default state. It will be argued that cancer is better understood as a disease of tissues rather than individual cells, and the complexities of tissues cannot be inferred from the study of cells in isolation. In-vitro studies which have been used to explain carcinogenesis will be critically reviewed and their relevance to in-vivo conditions will be questioned. Complex signaling mechanisms define the relationship between the epithelium and other cells in a metazoan tissue. These signals originate both from the stromal/mesenchymal compartments and between epithelial cells. Studies have shown that carcinogenic insults which affect the stroma alone can turn an otherwise normal epithelium cancerous, while transplanting “cancerous” epithelial cells into an otherwise normal stroma does not result in neoplasm formation. Experimental evidence has confirmed that the differentiation fate of any epithelial cell is malleable depending on its environmental context. Further, it was previously thought that epithelium had to dramatically change identity in order to be capable of migration. It will be shown that collective motility is an endogenous capability of epithelial cells, and multiple non-mammalian and mammalian in-vivo studies of collective epithelial motility will be reviewed to better understand epithelial motility in cancer. In fact, it will be shown that the creation of adhered epithelial sheets requires the same morphological changes necessary for motility. Lastly, evidence that heterogeneous cell populations contribute to epithelial cell migration in development and metastasis will be presented.

Insertion and deletion (indel), a common form of genetic variation, has been shown to cause or contribute to human genetic diseases and cancer. Despite this importance and being the second most abundant variant type in the human genome, indels have not been studied as much as the single nucleotide polymorphism (SNP). With the advance of next-generation sequencing technology, many indel calling tools have been developed. However, performance comparison of commonly used tools has shown that (1) the tools have limited power in identifying indels and there are significant number of indels undetected, and (2) there is significant disagreement among the indel sets produced by the tools. These findings indicate the necessity of improving the existing tools or developing new algorithms to achieve reliable and consistent indel calling results. Two indels are biologically equivalent if the resulting sequences are the same. Storing biologically equivalent indels as distinct entries in databases causes data redundancy and misleads downstream analysis. It is thus desirable to have a unified system for identifying and representing equivalent indels. This dissertation describes UPS-indel, a utility tool that creates a universal positioning system for indels so that equivalent indels can be uniquely determined by their coordinates in the new system. Results show that UPS-indel identifies more redundant indels than existing algorithms. While mapping short reads to the reference genome, a significant number of short reads are unmapped and excluded from downstream analyses, thereby causing information loss in the subsequent variant calling. This dissertation describes Genesis-indel, a computational pipeline that explores the unmapped reads to identify missing novel indels. Results analyzing sequence alignment of 30 breast cancer patients show that Genesis-indel identifies many novel indels that also show significant enrichment in oncogenes and tumor suppressor genes, demonstrating the importance of rescuing indels hidden in the unmapped reads in cancer and disease studies. Somatic mutations play a vital role in transforming healthy cells into cancer cells. Therefore, accurate identification of somatic mutations is essential. Many somatic mutations callers are available with different strengths and weaknesses. An ensemble approach integrating the power of the callers is warranted. This dissertation describes SomaticHunter, an ensemble of two callers, namely Platypus and VarDict. Results on synthetic tumor data show that for both SNPs and indels, SomaticHunter achieves recall comparable to the state-of-the-art somatic mutation callers and the highest precision, resulting in the highest F1 score. / Doctor of Philosophy / Insertion and deletion (indel), a common form of genetic variation in the human genome, is associated with genetic diseases and cancer. However, indels are heavily understudied due to experimental and computational challenges. This dissertation addresses the computational challenges in three aspects. First, the current approach of representing indels is ambiguous and causes significant database redundancy. A universal positioning system, UPS-indel, is proposed to represent equivalent indels unambiguously and the UPS-indel algorithm is theoretically proven to find all equivalent indels and is thus exhaustive. Second, a significant number of indels are hidden in DNA reads not mapped to the reference genome. Genesis-indel, a computational pipeline that explores the unmapped reads to identify novel indels that are initially missed, is developed. Genesis-indel has been shown to uncover indels that can be important genetic markers for breast cancer. Finally, mutations occurring in somatic cells play a vital role in transforming healthy cells into cancer cells. Therefore, accurate identification of somatic mutation is essential for a better understanding of cancer genomes. SomaticHunter, an ensemble of two sensitive variant callers, is developed. Simulated studies using whole genome and whole exome sequences have shown that SomaticHunter achieves recall comparable to state-of-the-art somatic mutation callers while delivering the highest precision and therefore resulting in the highest F1 score among all the callers compared.

No / Combinatorial antibody libraries were constructed from the spleen of a patient with concomitant systemic lupus erythematosus and idiopathic thrombocytopenia. Following selection of the libraries with DNA, a panel of 15 anti-DNA Fabs was isolated. Sequence analysis of these antibodies coupled with measurements of their affinities for ss- and dsDNA were used to investigate the role of somatic mutation in affinity maturation of the anti-DNA response. Examination of the germline genes used by these Fabs supports previous studies that suggest there is no restriction of the gene usage in the anti-DNA response. However, data are presented indicating that VH3 genes and the A27 V¿ paired with the J¿1 may be over-expressed in the anti-DNA repertoire. Analysis of the role of somatic mutation in increasing affinity for DNA indicates that affinity maturation has occurred and suggests that the CDR1 and CDR2 of the heavy chain are of importance in this process.

<p>Cerebral cavernous malformations (CCMs) are multicavernous vascular lesions affecting the central nervous system. Affected individuals have a lifetime risk of recurrent headaches, focal neurological deficits, seizures, and intracerebral hemorrhage leading to stroke. Patients tend to fall into two classes: familial cases with a known family history and multiple lesions, and; sporadic cases with no family history and single lesions. This epidemiological pattern suggests a two-hit mutational mechanism for CCM. While somatic mutations have been identified in lesions from familial patients, it is unknown if sporadic cases follow the same genetic mechanism. Using a next-generation sequencing strategy, I have identified somatic mutations from sporadic CCM lesions in the three known CCM genes, including one lesion bearing two independent mutations in CCM1. These data support a two-hit mutation mechanism in CCM for sporadic patients.</p><p>The mechanism of CCM pathogenesis (how mutations in one of the three CCM genes causes lesions to form and develop) is currently unknown. We developed mouse models that recapitulate the human disease. We have further shown that inhibition of Rho Kinase decreases the number of late-stage, multicavernous lesions. This is the first potential therapeutic strategy to specifically treat CCM, and suggests that the RhoA pathway is a central player in CCM pathogenesis.</p> / Dissertation

Breast cancer is the most common cancer in women worldwide. However, the genetic alterations that lead to breast cancer are not fully understood. This thesis aims to identify novel genes of potential mechanistic, diagnostic or therapeutic interest in breast cancers by mutational analysis and whole-genome sequencing. In paper I, sequencing of 36 previously identified candidate genes in 96 breast tumors with patient-matched normal DNA determined the somatic mutation prevalence of these candidate genes and identified additional mutations in Notch, NF-κB, PI3K, and Hedgehog pathways as well as in processes mediating DNA methylation, RNA processing and calcium signaling. In paper II, comparison of massively parallel mate-pair sequencing results of a human genome before and after phi29-mediated multiple displacement amplification (MDA) revealed that MDA introduces structural alteration artifacts, with an emphasis on false positive inversions, and impairs the sensitivity to detect true inversions. Therefore, MDA has limited value in sample preparation for whole-genome sequencing for structural alteration detection. In paper III, massively parallel paired-end sequencing identified gene rearrangements in 15 hormone receptor negative breast cancers. Forty validated rearrangements were predicted to directly affect 30 genes, involved in epigenetic regulation, cell mitosis, signalling transduction and glycolytic flux. RNA interference-based assays revealed the potential roles in cell growth of some affected genes, among which DDX10 was implicated to be involved in apoptosis. In paper IV, a method for statistical evaluation of putative translocations detected by massively parallel paired-end sequencing was proposed. In an application of this method to analyse translocations detected by cancer genome deep paired-end sequencing, 76 putative translocations were classified into four categories, with the majority likely to be caused by mismapping due to repetitive regions. Taken together, this thesis provides insights into genes and pathways mutated in sporadic breast cancer genomes, which broaden our understanding of the genetic basis of breast cancer and may ultimately facilitate the diagnosis and treatment of this disease.

Submitted by Natalia de Souza Gonçalves (natalia.goncalves@ufpe.br) on 2016-09-19T13:06:41Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação Mestrado-André-Severino-da-Silva-FINAL-2016 digital ok.pdf: 968681 bytes, checksum: 7aa8797460dde7f9b350d87b19110eee (MD5) / Made available in DSpace on 2016-09-19T13:06:41Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação Mestrado-André-Severino-da-Silva-FINAL-2016 digital ok.pdf: 968681 bytes, checksum: 7aa8797460dde7f9b350d87b19110eee (MD5) Previous issue date: 2016-02-23 / FACEPE / Compostos com núcleo pirimidínico têm grande potencial e importância farmacológica para a saúde humana, pois apresentam várias propriedades biológicas como atividade anti-inflamatória, antitumoral, bioherbicida, entre outras. Este trabalho busca analisar os efeitos genotóxicos dos compostos 4-Amino-2-(fenil)-6-(m-nitrofenil)-5-carbonitrila-pirimidina (5a), 4-Amino-2-(fenil)-6-(p-nitrofenil)-5-carbonitrila- pirimidina (5b) e 4-Amino-2-(fenil)-6-(p-anisil)-5-carbonitrila-pirimidina (5c), obtidos por síntese, por meio do teste SMART (Teste de Mutação e Recombinação Somática) e Ensaio Cometa em Drosophila melanogaster. Para o Ensaio Cometa, larvas de D. melanogaster da linhagem Oregon-R foram expostas por 24 horas aos compostos 5a, 5b e 5c, nas concentrações 0,39, 0,78, 1,56 e 3,12 mg/mL, e ao solvente (grupo controle negativo), além de um grupo controle positivo (Ciclofosfamida 1 mg/mL). Para a análise microscópica dos possíveis danos genéticos causados pelos compostos foram observadas as células da hemolinfa (hemócitos) de larvas. No processo metodológico do SMART, larvas de D. melanogaster foram expostas às concentrações 0,04, 0,09, 0,19, 0,39, 0,78, 1,56 e 3.12 mg/mL dos compostos 5a e 5b, além dos grupos controle negativo (tratado apenas com o solvente) e controle positivo (tratado com mitomicina 1mg/mL). Foi estabelecida uma curva de sobrevivência de acordo com o nascimento dos indivíduos adultos para verificar a citotoxicidade dos compostos. As manchas e pelos mutantes das asas dos indivíduos adultos tratados foram analisadas em microscópio óptico e comparados aos resultados do grupo controle negativo. Os resultados indicaram que não houve diferenças significativas entre os grupos tratados e os controles negativos, tanto para o teste SMART, quanto para o Ensaio Cometa. No teste SMART, as curvas de sobrevivência mostraram que os compostos 5a e 5b, não apresentaram toxicidade para os drosofilídeos testados. Podendo-se concluir, assim, que nas condições experimentais testadas em D. melanogaster os compostos não apresentaram atividade tóxica nem mutagênica, o que contribui para o uso dos compostos pirimidínicos aqui investigados na composição de novos fármacos para o tratamento da saúde humana. / Compounds of the core pyrimidine have great potential and pharmacological importance to human health and the environment and therefore exhibit different biological properties as anti-inflammatory, antitumor, bioherbicide among others. This work intent to analyze the genotoxic effects of the compounds 4-Amino-2-(phenyl)-6-(m-nitrophenyl)-5-carbonitrile-pyrimidine (5a) 4-Amino-2-(phenyl)-6-(p-nitrophenyl)-5-carbonitrile-pyrimidine (5b) and 4-Amino-2-(phenyl)-6-(p-anisyl)-5-carbonitrile-pyrimidine (5c) obtained by chemical synthesis using the SMART (Somatic Mutation and Recombination Test) and Comet Assay in Drosophila melanogaster. For SMART, D. melanogaster larvae were exposed to concentrations of 0.04, 0.09, 0.19, 0.39, 0.78, 1.56 and 3.12 mg/mL of the compounds 5a and 5b, and a negative control group treated only with the solvent. A survival curve was established in accordance with the birth of adults in order to check the cytotoxicity of the compounds. The spots and the mutants were analyzed by light microscopy and the results of the groups treated were compared to the negative control group. During the methodological process of the Comet Assay, larvae of D. melanogaster Oregon-R strain were exposed for 24 hours to the compounds 5a, 5b and 5c, at the concentrations 0.39, 0.78, 1.56 and 3.12 mg/mL, and to the solvent (the negative control group). To microscopic analysis of possible genetic damage caused by the compounds, were observed cells from the hemolymph (hemocytes) of larvae. The results indicated that in both tests there were no significant difference between the treated groups and the negative control. It leads us to conclude that the tested compounds showed neither toxic effect, nor mutagenic activity in D. melanogaster over the experimental conditions in D. melanogaster model.

L'exploitation de la variation clonale est une des voies d'amélioration utilisée chez un grand nombre de plantes d'intérêts agronomiques telles que la pomme de terre, le café et la vigne. En effet, après plusieurs cycles de reproduction végétative, des caractéristiques agronomiques stables apparaissent donnant naissance à une diversité phénotypique remarquable, appelée « diversité clonale ». Chez la vigne, cette diversité clonale est d'une importance majeure pour les viticulteurs puisqu'elle permet une amélioration variétale sans changer d'identité de cépage en conformité avec la réglementation fixée par Appellations d'Origine Protégée. L'hypothèse la plus parcimonieuse expliquant cette diversité phénotypique clonale est l'accumulation de mutations somatiques au cours des cycles de reproduction végétative. L'objectif de cette thèse a été de dresser un panorama le plus exhaustif possible des différents polymorphismes moléculaires entre les génomes de plusieurs clones. Dans un premier temps trois clones de Pinot ont été séquencés par la technique 454 GS-FLX puis dans un second temps 11 clones de quatre cépages ont été séquencés la technique Illumina HiSeq 2000. Afin d'analyser la grande quantité de données obtenues, nous avons construit un pipeline d'analyse (Bacchus pipeline) permettant d'identifier tous les types de polymorphismes moléculaires entre les différents génomes.Nos résultats permettent, pour la première fois un inventaire exhaustif des polymorphismes moléculaires dans un contexte multiplication végétatif. L'ensemble des mutations polymorphes entre deux clones a pu être identifié, SNPs, indels (2,5 SNPs et 11,5 indels par Mb en moyenne) ainsi que des variations d'ordre structural (larges insertions ou délétions) représentant la classe la plus fréquente (129 évènements par Mb entre deux clones en moyenne). Afin d'évaluer le polymorphisme d'insertion généré par ces éléments nous en avons étudié quatre par une approche S-SAP sur plusieurs niveaux de diversité (inter-espèces, inter-cépages, inter-clones et entre plusieurs tissus d'un même individu). L'analyse phylogénétique au niveau des espèces est conforme à celle réalisée avec d'autres types de marqueurs moléculaires (SSR, SNP). Cependant, une forte instabilité de ces insertions a été confirmée entre les clones et entre les tissus d'un même d'individu. L'identification des clones par une méthodologie moléculaire serait d'une grande importance pour la filère. Pour cet objectif, nos résultats indiquent que les mutations de types SNP et petits indels qui sont certes moins fréquentes que les variations structurales mais qui sont plus stables semblent plus pertinentes pour la mise en place d'une méthodologie d'identification des clones / Clonal variation is considered as an effective contribution to breeding programs of vegetatively propagated species with major agronomical interest such as banana, potato, coffee and grape. Indeed, after several propagation cycles, stable and heritable phenotypic variations appear giving rise to a phenotypic variation termed “clonal diversity”. This clonal diversity is very important for wine-growers because it allows preserving cultivars identity in the strict respect of Appellation (A.O.P) wines specifications The most parsimonious hypothesis explaining clonal phenotypic diversity is the accumulation of somatic mutations. The objective of my thesis was to provide a broad description of molecular polymorphisms in the context of vegetative propagation. Three clones were first sequenced by 454 GS-FLX technology and eleven clones were then sequenced with Illumina Hiseq2000 technique. To analyse the high quantity of data obtained, we built a pipeline (Bacchus pipeline) allowing the identification of all existing molecular polymorphisms between different genomes.All polymorphism types were observed: indels and SNPs which have a low polymorphism frequency (2.5 SNPs and 11.5 indels per Mb between two clones in average) and structural variations (large insertions or deletions) which have a high polymorphism frequency (129 per Mb between two clones in average) but are unstable. To evaluate stability and polymorphism level of these transposable elements, we have studied 4 elements using S-SAP method at different diversity levels (inter-species, inter-cultivars, inter-clones and between organs/tissues of a single individual). Our interspecific phylogenetic analysis is similar to other phylogenies performed with SSR or SNPs markers. However, we confirm the high instability of these elements between clones and between tissues in single individuals.Clone identification through molecular methods would be of high significance for the wine industry. SNP or small indels mutations are less frequent but more stable than structural variation and could be used for accurate clone identification.