<p>Preserving genome stability is critical to ensure the faithful transmission of intact genetic material through each cell division. One of the key components of this preservation is maintaining low levels of mutagenesis. Most mutations arise during replication of the genome, either as polymerase errors made when copying an undamaged DNA template or during the bypass of DNA lesions. Many different DNA repair proteins act both prior to and during replication to prevent the occurrence of these mutations. Although the mechanisms by which mutations occur and the various repair proteins that act to suppress mutagenesis are conserved throughout all species, they are best characterized in the yeast <italic>Saccharomyces cerevisiae</italic>. In this work, we have used this model system to study two types of spontaneous mutagenesis: oxidative mutagenesis and frameshift mutagenesis. In the first part of this work, we have examined mutagenesis that arises due to one of the most common oxidative lesions in the cell, 7,8-dihydro-8-oxoguanine or GO. When present during replication, these GO lesions generate characteristic transversion events that are accurately repaired by the mismatch repair pathway. We provide the first evidence that a second pathway involving the translesion synthesis polymerase Pol&eta acts independently of the mismatch repair pathway to suppress GO-associated mutagenesis. We have also examined how differences in replication timing during S phase contribute to variations in the rate of these mutations across the genome. In the second part of this work, we have examined how spontaneous frameshift mutations are generated during replication. While most frameshift mutations occur in regions of repetitive DNA, we have designed a system to examine frameshifts that occur in very short repeats (< 4 nucleotides) and noniterated sequences. We have examined the patterns of frameshifts at these sites and how the mismatch repair pathway acts to suppress these mutations. Together, the experiments presented here provide further insight into the different mechanisms that suppress and/or influence rates of oxidative mutagenesis and describe a system in which we have begun to characterize how frameshift mutations are generated at very short repeats and non-repetitive DNA.</p> / Dissertation

abstract: Immunotherapy has been revitalized with the advent of immune checkpoint blockade treatments, and neo-antigens are the targets of immune system in cancer patients who respond to the treatments. The cancer vaccine field is focused on using neo-antigens from unique point mutations of genomic sequence in the cancer patient for making personalized cancer vaccines. However, we choose a different path to find frameshift neo-antigens at the mRNA level and develop broadly effective cancer vaccines based on frameshift antigens. In this dissertation, I have summarized and characterized all the potential frameshift antigens from microsatellite regions in human, dog and mouse. A list of frameshift antigens was validated by PCR in tumor samples and the mutation rate was calculated for one candidate – SEC62. I develop a method to screen the antibody response against frameshift antigens in human and dog cancer patients by using frameshift peptide arrays. Frameshift antigens selected by positive antibody response in cancer patients or by MHC predictions show protection in different mouse tumor models. A dog version of the cancer vaccine based on frameshift antigens was developed and tested in a small safety trial. The results demonstrate that the vaccine is safe and it can induce strong B and T cell immune responses. Further, I built the human exon junction frameshift database which includes all possible frameshift antigens from mis-splicing events in exon junctions, and I develop a method to find potential frameshift antigens from large cancer immunosignature dataset with these databases. In addition, I test the idea of ‘early cancer diagnosis, early treatment’ in a transgenic mouse cancer model. The results show that ii early treatment gives significantly better protection than late treatment and the correct time point for treatment is crucial to give the best clinical benefit. A model for early treatment is developed with these results. Frameshift neo-antigens from microsatellite regions and mis-splicing events are abundant at mRNA level and they are better antigens than neo-antigens from point mutations in the genomic sequences of cancer patients in terms of high immunogenicity, low probability to cause autoimmune diseases and low cost to develop a broadly effective vaccine. This dissertation demonstrates the feasibility of using frameshift antigens for cancer vaccine development. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2018

The mismatch repair system (MMR) is an important pathway for maintaining genome stability because it can remove the errors generated while the cell is replicating. If these errors are left uncorrected, they can lead to genomic mutations. Thus, the deficient mismatch repair system is associated with the development of sporadic cancers and degenerative diseases such as Lynch Syndrome. MMR involves a set of proteins including MutSα, MutLα, MutLβ, and MutLγ. MutSα and MutLα play a major role in MMR whereas MutLβ and MutLγ provide minor contributions to this pathway. Recent studies have suggested that MutLβ and MutLγ are involved in the triplet DNA repeat expansion pathway. Our study in Saccharomyces cerevisiae shows important preliminary data of Mlh3 in maintaining genomic stability. We studied its interactions with other proteins involved in the mismatch repair system. Interestingly, Mlh3 interactions with Msh3 and Pol 35 DV suggest that there is a predilection of MutSβ and MutLγ to work in the lagging strand. Additionally, Top1, Mlh3and Msh3our results have shown that these genetic interactions could lead to an increase in mistakes in the MMR pathway. Moreover, it could lead to the suggestion that they are also involved in another pathway such as transcription. Finally, we confirm the involvement of Mlh3 in the resolution of frameshift mutations in the His-7A locus. Even though they are interesting results is too early to make final conclusions. Further analysis needs to be done.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

O complexo da esclerose tuberosa (TSC) é um transtorno genético, sistêmico, com expressividade variável e herança autossômica dominante. Clinicamente manifesta-se devido ao desenvolvimento de hamartomas e hamártias em diferentes tecidos, principalmente no cérebro, rins, coração, pele e pulmões, podendo causar disfunção do órgão. Mutação em um de dois genes supressores tumorais, TSC1 ou TSC2, são responsáveis pelo TSC. Os genes TSC1 e TSC2 codificam para hamartina e tuberina, respectivamente. Ambas as proteínas interagem fisicamente formando um complexo citosólico que inibe mTOR (mammalian target of rapamycin). Testes moleculares para TSC1 e TSC2 são úteis para auxiliar no diagnóstico de casos clínicos difíceis, em aconselhamento genético e estudos de associação genótipo-fenotípica, além de permitirem a caracterização molecular de mecanismos patogenéticos da formação dos hamartomas e análises funcionais de seus produtos gênicos. Apesar de o diagnóstico de TSC ser basicamente clínico, a partir da revisão de seus critérios em 2012 por um grupo de especialistas, o achado de uma mutação em TSC1 ou TSC2 passou a ser considerado suficiente para o diagnóstico definitivo da doença. O estudo apresentado aqui é parte de um projeto em andamento para estabelecer condições ao desenvolvimento de análise de mutações causadoras de TSC nos genes TSC1 e TSC2. Nosso objetivo neste trabalho foi avaliar por sequenciamento de Sanger o DNA genômico de 28 pacientes brasileiros com diagnóstico definitivo de TSC, procedentes dos estados de São Paulo ou Paraná, tendo como alvo a sequência codificadora do gene TSC1, parte de seus segmentos intrônicos, o promotor basal, bem como o segmento imediatamente a 5\' deste. Sete pacientes (25%) apresentaram mutações de sentido trocado (nonsense) ou com deslocamento da leitura à tradução (frameshift) no gene TSC1. Entre 31 outras variantes de DNA encontradas, 23 são polimorfismos conhecidos e oito apresentaram frequência inferior a 1%, como verificado in silico entre mais de mil sequências de genomas humanos. Entre essas oito variantes de DNA novas ou raras, quatro foram detectadas em pacientes para os quais uma mutação patogênica havia sido identificada e, por isso, foram reclassificadas como polimorfismos. Duas e uma variantes de DNA do mesmo paciente flanqueavam um sítio de ligação em potencial para um fator de transcrição específico, a 5\' do promotor basal de TSC1. Por fim, uma nova variante de DNA na região não codificadora do éxon 2 do gene TSC1 foi predita com potencial para alterar um elemento candidato a acentuador de splicing. Em resumo, como observado em estudos anteriores, descrevemos aqui 25% dos pacientes com TSC apresentando mutações patogênicas na sequência codificadora do gene TSC1. Nossos dados mostraram quatro novas variantes de DNA em regiões potencialmente reguladoras da expressão do gene TSC1, que podem revelar-se como mutações patogênicas e, portanto, necessitam ser testadas experimentalmente / Tuberous sclerosis complex (TSC) is a multisystem disorder, with variable expression and autosomal dominant inheritance. Clinically it is due to hamartia and hamartoma development in different tissues, notably in the brain, kidneys, heart, skin and lungs, causing organ dysfunction. Mutations in either tumor suppressor gene, TSC1 or TSC2, are responsible for TSC. TSC1 and TSC2 genes code for hamartin and tuberin, respectively. Both proteins physically interact forming a cytosolic complex that inhibits the mammalian target of rapamycin (mTOR). TSC1 and TSC2 molecular testing has been useful in diagnosing clinically challenging cases, in genetic counseling and genotype/phenotype association studies, besides evaluation of the molecular basis of hamartoma formation and functional analyses of both gene products. Although TSC diagnosis is basically clinical, since the 2012 specialist panel review the finding of a TSC1 or TSC2 mutation has been considered sufficient for the definite diagnosis of the disease. The results presented here are part of an ongoing project to establish conditions for TSC1 and TSC2 mutation studies. Our first aim is to evaluate by Sanger sequencing TSC1 coding sequence, and an average of 132 base pairs of intronic regions next to exon boundaries from TSC patients, in addition to the gene core promoter. We present preliminary results of a sample of 28 patients with definite TSC diagnosis, from São Paulo and Paraná states. Seven patients (25%) displayed TSC1 nonsense or frameshift mutations. Among 31 other DNA variants identified, 23 were known polymorphisms, and eight had frequencies below 1% as verified in silico among more than a thousand human genomes. Out of eight novel or rare DNA variants, four were detected in patients for whom a pathogenic mutation had been found. Two and one additional DNA point variants from the same patient flanked a putative transcription factor binding site. Finally, a novel DNA variant residing in the TSC1 noncoding exon 2 was predicted to change the sequence potential to behave as a splicing enhancer. In summary, similar to previous studies, we describe 25% of TSC patients with mutations in the TSC1 coding sequence. Differently from other reports, our data disclose four novel DNA variants in TSC1 potentially regulatory regions that are likely to unravel novel pathogenic mutations, and thus need to be experimentally tested

O complexo da esclerose tuberosa (TSC) é um transtorno genético, sistêmico, com expressividade variável e herança autossômica dominante. Clinicamente manifesta-se devido ao desenvolvimento de hamartomas e hamártias em diferentes tecidos, principalmente no cérebro, rins, coração, pele e pulmões, podendo causar disfunção do órgão. Mutação em um de dois genes supressores tumorais, TSC1 ou TSC2, são responsáveis pelo TSC. Os genes TSC1 e TSC2 codificam para hamartina e tuberina, respectivamente. Ambas as proteínas interagem fisicamente formando um complexo citosólico que inibe mTOR (mammalian target of rapamycin). Testes moleculares para TSC1 e TSC2 são úteis para auxiliar no diagnóstico de casos clínicos difíceis, em aconselhamento genético e estudos de associação genótipo-fenotípica, além de permitirem a caracterização molecular de mecanismos patogenéticos da formação dos hamartomas e análises funcionais de seus produtos gênicos. Apesar de o diagnóstico de TSC ser basicamente clínico, a partir da revisão de seus critérios em 2012 por um grupo de especialistas, o achado de uma mutação em TSC1 ou TSC2 passou a ser considerado suficiente para o diagnóstico definitivo da doença. O estudo apresentado aqui é parte de um projeto em andamento para estabelecer condições ao desenvolvimento de análise de mutações causadoras de TSC nos genes TSC1 e TSC2. Nosso objetivo neste trabalho foi avaliar por sequenciamento de Sanger o DNA genômico de 28 pacientes brasileiros com diagnóstico definitivo de TSC, procedentes dos estados de São Paulo ou Paraná, tendo como alvo a sequência codificadora do gene TSC1, parte de seus segmentos intrônicos, o promotor basal, bem como o segmento imediatamente a 5\' deste. Sete pacientes (25%) apresentaram mutações de sentido trocado (nonsense) ou com deslocamento da leitura à tradução (frameshift) no gene TSC1. Entre 31 outras variantes de DNA encontradas, 23 são polimorfismos conhecidos e oito apresentaram frequência inferior a 1%, como verificado in silico entre mais de mil sequências de genomas humanos. Entre essas oito variantes de DNA novas ou raras, quatro foram detectadas em pacientes para os quais uma mutação patogênica havia sido identificada e, por isso, foram reclassificadas como polimorfismos. Duas e uma variantes de DNA do mesmo paciente flanqueavam um sítio de ligação em potencial para um fator de transcrição específico, a 5\' do promotor basal de TSC1. Por fim, uma nova variante de DNA na região não codificadora do éxon 2 do gene TSC1 foi predita com potencial para alterar um elemento candidato a acentuador de splicing. Em resumo, como observado em estudos anteriores, descrevemos aqui 25% dos pacientes com TSC apresentando mutações patogênicas na sequência codificadora do gene TSC1. Nossos dados mostraram quatro novas variantes de DNA em regiões potencialmente reguladoras da expressão do gene TSC1, que podem revelar-se como mutações patogênicas e, portanto, necessitam ser testadas experimentalmente / Tuberous sclerosis complex (TSC) is a multisystem disorder, with variable expression and autosomal dominant inheritance. Clinically it is due to hamartia and hamartoma development in different tissues, notably in the brain, kidneys, heart, skin and lungs, causing organ dysfunction. Mutations in either tumor suppressor gene, TSC1 or TSC2, are responsible for TSC. TSC1 and TSC2 genes code for hamartin and tuberin, respectively. Both proteins physically interact forming a cytosolic complex that inhibits the mammalian target of rapamycin (mTOR). TSC1 and TSC2 molecular testing has been useful in diagnosing clinically challenging cases, in genetic counseling and genotype/phenotype association studies, besides evaluation of the molecular basis of hamartoma formation and functional analyses of both gene products. Although TSC diagnosis is basically clinical, since the 2012 specialist panel review the finding of a TSC1 or TSC2 mutation has been considered sufficient for the definite diagnosis of the disease. The results presented here are part of an ongoing project to establish conditions for TSC1 and TSC2 mutation studies. Our first aim is to evaluate by Sanger sequencing TSC1 coding sequence, and an average of 132 base pairs of intronic regions next to exon boundaries from TSC patients, in addition to the gene core promoter. We present preliminary results of a sample of 28 patients with definite TSC diagnosis, from São Paulo and Paraná states. Seven patients (25%) displayed TSC1 nonsense or frameshift mutations. Among 31 other DNA variants identified, 23 were known polymorphisms, and eight had frequencies below 1% as verified in silico among more than a thousand human genomes. Out of eight novel or rare DNA variants, four were detected in patients for whom a pathogenic mutation had been found. Two and one additional DNA point variants from the same patient flanked a putative transcription factor binding site. Finally, a novel DNA variant residing in the TSC1 noncoding exon 2 was predicted to change the sequence potential to behave as a splicing enhancer. In summary, similar to previous studies, we describe 25% of TSC patients with mutations in the TSC1 coding sequence. Differently from other reports, our data disclose four novel DNA variants in TSC1 potentially regulatory regions that are likely to unravel novel pathogenic mutations, and thus need to be experimentally tested

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

To increase diversity of enzymes and proteins, cells mix and match exonic and intronic regions retained in mature mRNAs by alternative splicing. An estimated 94% of all multi-exon genes express one or more alternatively spliced transcripts generating proteins with similar or modified functions. Cyclooxygenase is a signaling enzyme that catalyzes the rate-limiting step in the synthesis of diverse bioactive lipids termed prostaglandins. Prostaglandins are involved in myriad physiological and pathopysiological processes including vasoregulation, stomach mucosal maintenance, parturition, pain, fever, inflammation, neoplasia and angiogenesis and are inhibited by aspirin-like drugs known as NSAIDs. In 2002 an alternatively spliced, intron-1 retaining variant of COX-1 was cloned from canine brain tissue. This new variant, termed COX-3 or COX-1b, is an enzymatically active prostaglandin synthase expressed at relatively high levels in a tissue and cell type dependant manner in all species examined. In humans and most rodent species intron-1 is 94 and 98 nucleotides long respectively. Retention of the intron in these species introduces a frameshift and is predicted to result in translation of a very small 8-16kD protein with little similarity to either 72kD COX-1 or COX-2, calling into question the role of this variant. In this dissertation, I present my results from cloning and ectopically expressing a complete and accurate COX-3 cDNA from both rat and human. I confirmed that COX-3 mRNA encodes multiple large molecular weight cyclooxygenase-like proteins in the same reading frame as COX-1. Translation of these proteins relies on several recoding mechanisms including cap-independent translation initiation, alternative start site selection, and ribosomal frameshifting. Using siRNA and Western blotting I have identified some of these proteins in tissues and cells. Two COX-3 encoded proteins are active prostaglandin synthase enzymes with activities similar to COX-1 and represent novel targets of NSAIDs. Other COX-3 proteins have unknown function, but their size and cellular location suggest potential roles as diverse as cytosolic enzymes and nuclear factors.

Many viruses can produce multiple proteins from a single mRNA sequence by encoding the proteins in overlapping genes. One mechanism that causes the ribosomes of infected cells to decode both genes is –1 programmed ribosomal frameshifting. In this process, structural elements of the viral mRNA signal the ribosome to shift reading frames at a specific point. Although –1 frameshifting has been recognized since 1985, the mechanism is not well understood. I have developed a stochastic model of mRNA translation that includes the possibility of a –1 frameshift at any codon. The transition probabilities between states of the model are based on the energetics of local molecular interactions. The model reproduces observed translation rates as well as both the location and efficiency of frameshift events in the HIV-1 gag-pol sequence. In this work, the model is used to predict changes in the frameshift efficiency due to mutations in the viral mRNA sequence or variations in relative tRNA abundances. The model is sensitive to the size of the translating ribosome and to assumptions about the unfolding pathway of the stimulatory structure. As knowledge in the field of RNA structure prediction grows, that knowledge can be incorporated into the model developed here to make improved predictions. The single-ribosome translation model has been extended to polysomes by including initiation and termination rates and an exclusion principle, and allowing the stimulatory structure to refold on an appropriate timescale. The predicted frameshift efficiency for a given mRNA can be tuned by varying the ribosome density on the mRNA. This finding affects the interpretation of frameshift efficiencies measured in the lab. In the parameter regime where translation is initiation-limited, the frameshift efficiency also depends on the structure refolding rate, which determines the availability of the downstream structure for stimulating –1 frameshifts. Furthermore, there is a trade-off between frameshift efficiency and protein synthesis rate.