Germline mutations in mismatch repair genes predispose individuals to Lynch Syndrome, the most common colorectal cancer predisposition syndrome. MLH1 is a key mismatch repair gene that is mutated in Lynch syndrome and about a third of the genetic alterations identified in MLH1 are missense variants of unclassified clinical significance. We hypothesize that missense alterations in distinct domains of MLH1 likely affect its expression and function(s) to varying degrees. To address this we utilized several approaches to investigate the molecular basis of the pathogenicity of a panel of unclassified variants. Our results demonstrate that the MLH1 variants p.R265C and p.K618A significantly decrease the stability of the MLH1 protein, while the variant p.L749Q compromises heterodimerization of the MLH1-PMS2 complex. Given the limitations and complexity of in vitro assessment strategies, we conducted a proof-of-principle study to investigate whether missense variants in MLH1 lead to allelic imbalances at the transcriptional level. Our analysis using the PeakPicker software indicated that the missense variants c.350C>T, c.793C>T, c.1852_1853AA>GC, as well as the truncating variant c.1528C>T were associated with significantly unbalanced allelic expression. This illustrates a novel method of investigating the pathogenicity of unclassified genetic variants, which has the potential to be applied in the diagnostic setting. Previous genetic epidemiology studies from our laboratory have demonstrated that the MLH1 c.-93G>A promoter variant is strongly associated with the microsatellite instability phenotype in colorectal tumours. Additionally, this promoter variant was associated with an elevated risk of endometrial cancer in case-control studies. Results from our functional studies indicate that the c.-93G>A variant significantly alters the promoter activity of MLH1. The MLH1 promoter is bi-directional with the EPM2AIP1 gene located on the antisense strand. Interestingly, we observed that this variant significantly affected EPM2AIP1 transcription as well. Furthermore, our experiments suggest that c.-93G>A variant affects transcription by altering the affinity of nuclear factors that bind this region. Combined, these findings shed light on the possible mechanisms by which missense variants affect MLH1 expression and function, which in conjunction with results from other functional assays will help increase the accuracy and efficiency of genetic testing of inherited cancers.

Germline mutations in mismatch repair genes predispose individuals to Lynch Syndrome, the most common colorectal cancer predisposition syndrome. MLH1 is a key mismatch repair gene that is mutated in Lynch syndrome and about a third of the genetic alterations identified in MLH1 are missense variants of unclassified clinical significance. We hypothesize that missense alterations in distinct domains of MLH1 likely affect its expression and function(s) to varying degrees. To address this we utilized several approaches to investigate the molecular basis of the pathogenicity of a panel of unclassified variants. Our results demonstrate that the MLH1 variants p.R265C and p.K618A significantly decrease the stability of the MLH1 protein, while the variant p.L749Q compromises heterodimerization of the MLH1-PMS2 complex. Given the limitations and complexity of in vitro assessment strategies, we conducted a proof-of-principle study to investigate whether missense variants in MLH1 lead to allelic imbalances at the transcriptional level. Our analysis using the PeakPicker software indicated that the missense variants c.350C>T, c.793C>T, c.1852_1853AA>GC, as well as the truncating variant c.1528C>T were associated with significantly unbalanced allelic expression. This illustrates a novel method of investigating the pathogenicity of unclassified genetic variants, which has the potential to be applied in the diagnostic setting. Previous genetic epidemiology studies from our laboratory have demonstrated that the MLH1 c.-93G>A promoter variant is strongly associated with the microsatellite instability phenotype in colorectal tumours. Additionally, this promoter variant was associated with an elevated risk of endometrial cancer in case-control studies. Results from our functional studies indicate that the c.-93G>A variant significantly alters the promoter activity of MLH1. The MLH1 promoter is bi-directional with the EPM2AIP1 gene located on the antisense strand. Interestingly, we observed that this variant significantly affected EPM2AIP1 transcription as well. Furthermore, our experiments suggest that c.-93G>A variant affects transcription by altering the affinity of nuclear factors that bind this region. Combined, these findings shed light on the possible mechanisms by which missense variants affect MLH1 expression and function, which in conjunction with results from other functional assays will help increase the accuracy and efficiency of genetic testing of inherited cancers.

No description available.

Em sua maioria, estratégias de transferência gênica utilizam arranjos com promotores e transgenes funcionando de maneira independente entre si, como é o caso do amplamente utilizado promotor CMV. Nosso grupo foge dessa linha de promotores/transgenes independentes. Desenvolvemos uma nova estratégia de transferência gênica que combina estrategicamente a atividade do transgene e o do promotor de expressão gênica, onde o promotor foi modificado com a inserção do elemento PG, responsívo a p53. Neste trabalho construímos um novo vetor adenoviral (AdPGp53) contendo o gene da proteína supressora de tumor p53 cuja expressão é controlada por ela própria através do elemento PG. Em comparação com um vetor adenoviral que possui o gene da p53 sob ação do promotor tradicional CMV (AdCMVp53), o vetor AdPGp53 apresentou expressão superior de p53 em células humanas de carcinoma de próstata PC3, maior morte celular in vitro e parece ter diminuído o ritmo de crescimento tumoral in vivo em um modelo xenográfico de células PC3 em camundongos atímicos. / The majority of gene therapy strategies in use today are based on promoters and transgenes that work independently, and an example of this is the widely used CMV promoter. Our group breaks way from the use of independent promoter/transgene activity. We developed a new gene transfer strategy which combines the transgene activity and the promoter of gene expression. This was achieved by the insertion of the PG element, which is a p53-responsive enhancer, in the promoter. In the present work we built a new adenoviral vector (AdPGp53) containing the p53 tumor suppressor gene, whose expression is controlled by the p53 protein itself through the PG element. In comparative experiments, in which we used our AdPGp53 vector and another adenoviral vector, with a p53 gene and a traditional CMV promoter (AdCMVp53), our vector showed superior p53 expression in PC3 human prostate cancer cells, superior cell death in vitro and a tendency in diminishing tumor growth in an in vivo xenograft model in nude mice injected with PC3 cells.

Dentre todos os tipos de câncer, excluindo-se o câncer de pele do tipo não melanoma, o de mama é o mais frequente em mulheres, sendo a segunda maior causa de morte por neoplasias nesse segmento da população. Em determinadas famílias, a incidência de câncer é superior à esperada para a população em geral, devido principalmente ao compartilhamento de fatores ambientais e/ou mutações genéticas responsáveis por facilitar ou dirigir a oncogênese. Os indivíduos que apresentam câncer de mama e histórico familial dessa patologia são descritos dentro do grupo câncer de mama familial (CMF), responsável por aproximadamente 5 a 10% do total de casos de câncer de mama. Atualmente, pacientes com CMF são frequentemente testados para mutações nos genes BRCA1 e BRCA2. Entretanto, estima-se que as variantes patogênicas presentes nos dois genes são responsáveis por somente 20% dos casos de CMF em que a etiologia genética é conhecida. Com relação aos testes genéticos para predisposição hereditária ao câncer de mama, torna-se relevante, portanto, a reavaliação da constituição dos painéis multigênicos frente ao estado do conhecimento científico atual, contemplando-se as mais recentes atualizações acerca dos genes e variantes genéticas associadas ao CMF. Neste trabalho, realizamos uma revisão bibliográfica que identificou 45 genes com associação estatística ao CMF, dentre eles 16 são frequentemente avaliados em painéis multigênicos brasileiros e internacionais. Em análise in silico, avaliamos as funções celulares e interações entre os produtos gênicos associados à patologia. Nossos resultados sugerem a adição de oito genes à composição de painéis multigênicos realizados no Brasil, EUA e Europa para avaliação da predisposição hereditária ao câncer de mama. Essa análise crítica pode auxiliar o aprimoramento de estratégias de prevenção, triagem, manejo clínico e determinação do risco de ocorrência e recorrência, com impactos sobre o aconselhamento genético (AG) oferecido aos pacientes afetados pelo câncer familial e seus familiares. Complementarmente, avaliamos as variantes gênicas presentes em pacientes com câncer de mama que realizaram o painel multigênico para predisposição hereditária ao câncer no Centro de Pesquisa sobre o Genoma Humano e Células-Tronco (CEGH-CEL). As frequências de mutações da coorte do CEGH-CEL são semelhantes às obtidas em estudos internacionais, possibilitando a utilização de painéis multigênicos com composições similares em populações de diversas localidades / Of all types of cancer, except for non-melanoma skin cancer, breast cancer is the most common among women, and it\'s the second leading cause of death by neoplasia in this segment of the population. In some families, the incidence rates of cancer are higher than expected for the general population because of the environmental factors and/or genetic mutations responsible for facilitating or driving oncogenesis. The individuals who have breast cancer and a family history of this pathology fall into the group of familial breast cancer (FBC), which is responsible for approximately 5-10% of all breast cancer cases. Currently, patients with FBC are frequently tested for mutations in the BRCA1 and BRCA2 genes. It is estimated, however, that the pathogenic variants of these genes account for only 20% of all FBC cases in which the genetic etiology is known. In relationship to the genetic tests for inherited predisposition for breast cancer, therefore it is relevant to reassess the multi-gene panel composition, considering the state of scientific knowledge today, including the most recent research on the genes and its variants associated with FBC. In this paper we did a literature review, which identified 45 genes statistically associated with FBC, out of which 16 are frequently assessed in multi-gene panels in Brazil and abroad. Through in silico analysis we were able to evaluate cell functions and interactions with gene products associated with cancer. Our results suggest the addition of eight genes to the multi-gene panel composition carried out in Brazil, in the USA and in Europe to assess hereditary predisposition to breast cancer. This critical analysis can assist in the development of preventive actions, triage, clinical management and in determining the risk of occurrence and recurrence, which impacts on the genetic counseling (GC) offered to the patients of familial cancer and their relatives. Additionally, we evaluated the genetic variants in patients diagnosed with breast cancer who have undergone multi-gene panel testing for hereditary predisposition to cancer at the Centro de Pesquisa sobre o Genoma Humano e Células-Tronco (CEGH-CEL). These cohort\'s mutation frequencies are similar to the results in international studies, which could enable the use of multi-gene panels with similar compositions in populations from various locations

Notch receptors and ligands are type I transmembrane proteins that regulate development and differentiation during cell-cell contact. There are four Notch receptor homologues and five notch ligands, identified in humans till date. Upon ligand activation, Notch1 intracellular domain (NIC-1) is released into the cytoplasm, which binds to several proteins as well as translocates into the nucleus to effect the Notch signaling. In the absence of the activated Notch signaling, the Notch target genes are kept repressed by the transcriptional repressor C protein binding factor 1 (CBF1) also known as RBPjk or CSL for CBF1/Su(H)/Lag1. RBPjk binds to the sequence “CGTGGGAA” and acts as a constitutive repressor. Upon ligand dependent activation, NIC-1 enters into the nucler and converts RBPjk from transcriptional repressor to an activator. Notch binding to CSL replaces the SMRT corepressor complex with a coactivator complex including SKIP, Mastermind like 1 (MAML1) (Mastermind in Drosophila), and histone acetyl transferases PCAF, GCN5 and p300 activating the transcription of target genes. Mastermind-like (MAML), a family of transcriptional activator proteins comprising of 3 members 1 to 3, has been shown to be required for Notch signaling. MAML forms a ternary complex with RBPjk-NIC by directly interacting with NIC. In turn, MAML recruits the histone acetyl transferase p300/CBP, which acetylates the histones, thereby altering the structure of chromatin amenable for transcription. Activation of Notch pathway induces oncogenesis, which can be divided into two categories including 1) Inhibition of Apoptosis and 2) Induction of proliferation. In T cells, activation of Notch1 protects cells from T cell receptor, dexamethasone and etoposide-mediated apoptosis, Fas receptor-mediated signaling by up regulating IAP (Inhibitor of Apoptosis) and Bcl-2 families, as well as FLIP (FLICE-like inhibitor protein). Notch signaling also promotes the survival of T cells through maintenance of cell size as well as through the promotion of glucose uptake and metabolism. Notch-1 has been shown to protect against anoikis (apoptosis induced by matrix withdrawal) or p53-mediated apoptosis in immortalized epithelial cells, T cell receptor-induced apoptosis in mature cells and dexamethasone-mediated apoptosis in thymocytes. This study was carried out to functionally characterize NIC-1 (human Notch1-intracellular domain) as an inhibitor of apoptosis and to evaluate the therapeutic potential of reversal of this apoptosis inhibition. The main objectives of this study are 1. Construction of recombinant adenovirus expressing human Notch1-intracellular domain (Ad-NIC-1) and characterization of NIC-1 as an inhibitor of chemotherapy and p53-induced cytotoxicity and apoptosis. 2. Role of PI3 kinase -Akt/PKB -mTOR pathway in NIC-1-mediated inhibition of p53-induced apoptosis. 3. Essential role of association between mTOR and NIC-1 and the dependent NIC-1 phosphorylation in Notch1-mediated transcription and survival signaling. 4. Identification of NIC-1 as an inhibitor of E1A-induced apoptosis and the role of mTOR in NIC-1-mediated inhibition of E1A-induced apoptosis. Activated Notch1 was first linked to tumorigenesis through identification of a recurrent t(7;9)(q34;q34.3) chromosomal translocation involving the human Notch1 gene that is found in a subset of human pre-T-cell acute lymphoblastic leukemia’s (T-ALL). Deregulated Notch signaling is oncogenic, inhibits apoptosis and promotes survival. In order to understand survival signaling induced by Notch1 and its possible role in chemoresistance, we have generated a replication deficient recombinant adenovirus expressing human Notch1-intracellular domain (Ad-NIC-1) and shown that it produces functional NIC-1 protein. Using this overexpression system, we characterized that activated Notch1-inhibits chemotherapy and in particular p53 induced apoptosis. Notch1-mediated inhibition of p53-induced apoptosis does not include coactivator squelching. p53 was inefficient in binding to its DNA in NIC-1 overexpressing cells. The levels of phosphorylation at Ser15, Ser20, and Ser392 of p53 expressed from Ad-p53 significantly reduced in NIC-1 preinfected cells. These results suggest that NIC-1-mediated inhibition of p53-mediated apoptosis involves reduced DNA binding, reduced nuclear localization and reduced post translational modifications and thus reduced transactivation of its target genes. Notch1-mediated inhibition of p53 was found to occur mainly through mammalian target of rapamycin (mTOR) using PI3 kinase-Akt/PKB pathway, as the mTOR inhibitor; rapamycin treatment was able to reverse Notch-1 mediated inhibition of p53 and chemoresistance. Consistent with this, rapamycin failed to reverse NIC-1 induced chemoresistance in cells expressing rapamycin resistant mTOR. Our results also suggest that the N-terminal HEAT repeat and the kinase function of mTOR are essential for Notch mediated inhibition of p53. Further, ectopic expression of eIF4E, a translational regulator that acts downstream of mTOR, inhibited p53-induced apoptosis and conferred protection against p53-mediated cytotoxicity to similar extent as that of NIC-1 overexpression, but was not reversed by rapamycin, which indicates that eIF4E is the major target of mTOR in Notch1-mediated survival signaling. Notch1-intracellular domain (NIC-1), following proteolytic cleavage, binds to RBPjk and regulates transcription. Active NIC-1 located in the nucleus is phosphorylated, which makes it more stable and bind better to RBPjk. NIC-1 was also shown to bind to Deltex1 in the cytoplasm. Next, we studied the requirement of components of Notch1 signaling pathway for this function. By using variety of approaches, we found that both RBPjk and Maml1 and hence transcription activation is required for NIC-1-mediated survival signaling and inhibition of p53 functions. Interestingly, while we found the other Notch1 effector, Deltex1 is also required for above functions, Notch1 failed to activate PI3 kinase -Akt/PKB -mTOR pathway in Deltex1, but not in RBPjk silenced cells. Our results suggest that Notch-Deltex1 pathway activates PI3 kinase. Previous studies show that NIC-1 interacts with Deltex1 and Grb2 interacts with PI3 kinase. Our data shows that Deltex1 interacts with SH3 domain of Grb2. Since Notch1-Deltex1 and PI3 kinase-Grb2 interactions are known, we conclude that Notch1 activation of PI3 kinase involves Deltex1 and Grb2. We found activated mTOR was able to binds to NIC-1 and regulates its phosphorylation. Inhibition of mTOR either by PI3 kinase inhibitors or mTOR inhibitor treatment or silencing of Akt/PKB or mTOR reduced the phosphorylation of NIC-1 with the concomitant reduction in NIC-1-mediated transcription. Further, endogenous Notch1 receptor activated by the DSL ligand failed to activate transcription efficiently in rapamycin treated cells, implying a positive role for mTOR in mammalian Notch signaling. These studies reveal that Notch1 activates PI3 kinase -Akt/PKB -mTOR signaling through Deltex1 and subsequently activated mTOR modulates Notch1 signaling by direct binding and possibly thorough phosphorylation of the intracellular domain of Notch. Adenoviral E1A, in the absence of cooperating oncogene, suppresses primary tumor growth and reverses the transformed phenotype of human tumor cells by inducing apoptosis. E1A requires p53 for efficient induction of apoptosis and was shown to induce apoptosis by down regulating Akt and the activation of pro apoptotic factor p38 MAP kinase. Since our results suggest Notch1 inhibits chemotherapy and p53-induced apoptosis, we analyzed the ability of Notch1 to protect cells from E1A-induced apoptosis. Here we show that NIC-1 suppresses the ability of E1A to induce apoptosis. NIC-1 requires mTOR-dependent signal to inhibit E1A-mediated apoptosis, as the rapamycin, an mTOR inhibitor was able to completely reverse the ability of Notch1 to protect cells against E1A-induced apoptosis. The role of mTOR in NIC-1-mediated survival signaling was further confirmed by using the cells stably expressing rapamycin resistant mTOR. Rapamycin was able to reverse Notch1-mediated protection in cells expressing wild type mTOR but not in rapamycin resistant mTOR expressing cells. We also found that E1A was able to induce apoptosis in cells silenced for the pro apoptotic factor p38 and NIC-1 continued to inhibit E1A-induced apoptosis in these cells. These results confirm that Notch1 requires the activation of mTOR signaling but not p38 MAP kinase for inhibition of E1A-induced apoptosis. These results also suggest that the combination therapy utilizing E1A-mediated gene delivery in combination with inhibition of mTOR pathway may prove successful in treating Notch overexpressing cancers. Chemotherapy remains a major treatment modality for human cancers. Chemoresistance is a clinical problem that severely limits treatment success. It can be divided into two forms: intrinsic and acquired. Intrinsic resistance is the essence of oncogenic transformation, resulting from activation of oncogenes and the loss of tumor suppressors, and manifests itself as alterations in cell cycle checkpoints and apoptotic pathways. It is now widely accepted that the apoptotic capacity of the cancer cell is crucial in determining the response to chemotherapeutic agents. Indeed, several gene products that regulate apoptosis, i.e., p53, Akt and PI3K are frequently altered in cancer cells. In this study, we identified that cells with aberrant Notch1 signaling are chemoresistant. Activated Notch1 overexpression makes cells resistant to chemotherapy in a wild type p53 dependent manner. Notch protected p53 wild type cells but not p53 mutated or p53 deleted cells against chemotherapy induced cytotoxicity. Further, inactivation of p53 by specific silencing abrogated the ability of NIC-1 to protect H460 cells against adriamycin induced cytotoxicity. Most importantly, NIC-1 mediated chemoresistance can be reversed by blocking PI3 kinase -Akt/PKB -mTOR pathway. Collectively, these results suggest that cancers with activated Notch1 signaling are chemoresistant and provide basis for the reversal of chemoresistance.

Em sua maioria, estratégias de transferência gênica utilizam arranjos com promotores e transgenes funcionando de maneira independente entre si, como é o caso do amplamente utilizado promotor CMV. Nosso grupo foge dessa linha de promotores/transgenes independentes. Desenvolvemos uma nova estratégia de transferência gênica que combina estrategicamente a atividade do transgene e o do promotor de expressão gênica, onde o promotor foi modificado com a inserção do elemento PG, responsívo a p53. Neste trabalho construímos um novo vetor adenoviral (AdPGp53) contendo o gene da proteína supressora de tumor p53 cuja expressão é controlada por ela própria através do elemento PG. Em comparação com um vetor adenoviral que possui o gene da p53 sob ação do promotor tradicional CMV (AdCMVp53), o vetor AdPGp53 apresentou expressão superior de p53 em células humanas de carcinoma de próstata PC3, maior morte celular in vitro e parece ter diminuído o ritmo de crescimento tumoral in vivo em um modelo xenográfico de células PC3 em camundongos atímicos. / The majority of gene therapy strategies in use today are based on promoters and transgenes that work independently, and an example of this is the widely used CMV promoter. Our group breaks way from the use of independent promoter/transgene activity. We developed a new gene transfer strategy which combines the transgene activity and the promoter of gene expression. This was achieved by the insertion of the PG element, which is a p53-responsive enhancer, in the promoter. In the present work we built a new adenoviral vector (AdPGp53) containing the p53 tumor suppressor gene, whose expression is controlled by the p53 protein itself through the PG element. In comparative experiments, in which we used our AdPGp53 vector and another adenoviral vector, with a p53 gene and a traditional CMV promoter (AdCMVp53), our vector showed superior p53 expression in PC3 human prostate cancer cells, superior cell death in vitro and a tendency in diminishing tumor growth in an in vivo xenograft model in nude mice injected with PC3 cells.

Prostate cancer is the most common cancer among men. The purpose of this quantitative, meta-analysis study was to examine one-carbon metabolism gene polymorphisms in a group of genes to determine their association with prostate cancer risk. The genetic epidemiology theory provided the framework for the study. The data collected were from published articles. From over 2,800 individual studies, 20 articles were retained for results and data abstraction, following the title, abstract screen, and full text screening in the second phase. The data were analyzed by a meta-analysis statistical method, combining the results from selected studies to estimate the overall association. According to study results by the adjusted p-values of fixed model, there was a significant association between decreased risk of prostate cancer and the variant of Allele T, Genotype TT, and the recessive model of C667T polymorphism. In the random model, the adjusted p-values show a significant association between decreased risk of prostate cancer, the variant of Genotype TT, and recessive model. There was an increased risk of prostate cancer in A1298C polymorphism by adjusted p-value on the variant of Genotype AC, in the fixed model. This study leads to positive social change by providing information on an optimization surveillance strategy to ensure valid screening test for prostate disease reporting. Future studies with a greater number of samples are needed, including gene-gene and gene-environment interaction to verify study results.

<p>Mass spectrometry (MS) can provide rapid, sensitive, and specific analysis, making it a valuable tool to characterize biomolecules, especially their dynamic changes when involved in significant processes.  Compared to other analytical techniques, which mostly focus on solution-phase or solid-phase characterization, MS enjoys a more general and efficient detection of gas-phase analytes since it ultimately measures abundances of bare ions in vacuum. This unique detection capability of MS has been demonstrated, in this dissertation, by characterizing the neutral serine octamer, a gas-phase amino acid cluster that has been detected by MS only so far. Besides its existence, the progress of chiral enrichment has also been monitored and quantified by MS during octamer formation. The acquired MS data is crucial to interpreting the mechanism of chiral enrichment achieved by serine octamer and might suggest its involvement in the prebiotic world to eventually achieve biohomochirality. The work also showcases the capability of detecting neutral compounds by MS, which breaks the stereotype that MS is exclusively an ion-based technique. </p> <p><br></p> <p>Besides process monitoring in the open air, MS also monitors the highly complicated metabolism processes inside biosamples, primarily benefiting from its excellent sensitivity, specificity, and throughput of ion detection. Since altered cellular metabolism is being recognized as a hallmark of cancer, MS is suitable for cancer diagnostics, whose performance of diagnosing glioma, a common brain cancer, has been tested.  Desorption electrospray ionization(DESI) has been used as it avoids sample preparation and allows direct characterization of raw tissue, therefore well suited for on-site analysis such as in the operating room. In short, we have applied intraoperative DESI-MS analysis on raw brain biopsies to provide glioma diagnostics within 5 min. Specifically, the molecular features revealed by MS are translated into pathological information of analyzed tissue, like genetic mutations and tumor concentrations, which is highly desired during surgeries to guide tumor resection and improve patient management. </p> <p><br></p> <p>Knowledge of diagnostic biomarkers is essential to the translation from MS data to pathology, which can be obtained by metabolic profiling using MS. Despite the tradeoff between comprehensive characterization and analysis time, we have extensively explored endogenous metabolites by using tandem MS and expedited analysis by avoiding the use of chromatography. After fast profiling, statistical analysis of all MS features has been applied to discover diagnostic markers to distinguish healthy brain tissue from cancerous tissue. DESI-MS methods have been developed to facilitate a simple and rapid characterization of these biomarkers in tissue for a smooth clinical transition. </p> <p><br></p> <p>However, the complete characterization of endogenous metabolites in a complicated biomixture, like tissue, is challenging, especially without the orthogonal separation provided by chromatography. This unmet demand calls for the development of novel MS scans to improve the metabolite coverage. For lipidomics by direct infusion MS, the MS scans used for lipid profiling have not been greatly expanded since its introduction. These conventionalMS scans only target one structural moiety of lipids and leave the rest unresolved, which limits the structure elucidation and biological interpretation of diagnostic lipids. We have introduced additional lipid scans that target both the lipid headgroup and one fatty acyl chain, leaving the other fatty acyl chain flexible. These scans with higher specificity can further alleviate the matrix effect by uncovering fewer ions in each scan and provide more structural information to support lipid identification. As a proof-of-concept, we have used them to profile both common phospholipids and the rarer ether lipids that display significant variations between healthy mice tissue and those with metabolic syndrome. The additional structural information provided by these scans ensures a clear message expressed by the disease metabolism and potentially indicates invention points and therapeutic candidates.</p>

Abstract Hereditary mutations in DNA damage response (DDR) genes often lead to genomic instability and ultimately tumor development. However, the molecular mechanism of how these DDR deficiencies promote genomic instability and malignancy is not well understood. Thus, the specific aim of this thesis is to identify the functional and molecular framework behind the elevated breast cancer risk observed in heterozygous PALB2 and ABRAXAS mutation carriers. The heterozygous germline alteration in PALB2 (c.1592delT) causes a haploinsufficiency phenotype in the mutation carrier cells. Due to PALB2 haploinsufficiency, elevated Cdk activity and consequently aberrant DNA replication/damage response was observed in the PALB2 mutation carrier cells. Excessive origin firing that is indicative of replication stress was also seen in the PALB2 mutation carrier cells. In addition to replication stress, PALB2 mutation carrier cells also experience G2/M checkpoint maintenance defects. The increased malignancy risk in females associated with heterozygosity for the Finnish PALB2 founder mutation is likely to be due to aberrant DNA replication, elevated genomic instability and multiple different cell cycle checkpoint defects. The heterozygous germline alteration in ABRAXAS (c.1082G&#62;A) causes a dominant-negative phenotype in the mutation carrier cells. Decreased BRCA1 protein levels as well as reduced nuclear localization and foci formation of BRCA1 and CtIP was observed in the ABRAXAS mutation carrier cells. This causes disturbances in basal BRCA1-A complex localization, which is reflected by a restraint in error-prone DNA double-strand break (DSB) repair pathway usage, attenuated DNA damage response, deregulated G2/M checkpoint control and apoptosis. Most importantly, mutation carrier cells display a change in their transcriptional profile, which we attribute to the reduced nuclear levels of BRCA1. Thus, the Finnish ABRAXAS founder mutation acts in a dominant-negative manner on BRCA1 to promote genome destabilization in the heterozygous carrier cells. / Tiivistelmä Perinnölliset muutokset DNA-vauriovasteen geeneissä johtavat usein genomin epävakauteen ja lopulta syövän kehittymiseen. Molekyylitason mekanismeja, joilla vauriovasteen vajaatoiminta ajaa genomin epävakautta ja syöpää, ei kuitenkaan ymmärretä kunnolla. Tämän väitöskirjan tavoitteena on tunnistaa solutoiminnan ja molekyylitason vaikuttajat heterotsygoottisten PALB2- ja ABRAXAS-geenimuutosten kantajien kohonneen rintasyöpäriskin taustalla. Heterotsygoottinen ituradan suomalainen perustajamuutos PALB2-geenissä (c.1592delT) aiheuttaa haploinsuffisienssin kantajahenkilöiden soluissa. PALB2:n haploinsuffisienssin seurauksena kantajasoluissa havaittiin kohonnutta Cdk-proteiinin aktiivisuutta ja siitä johtuvaa kiihtynyttä DNA:n kahdentumista. PALB2-mutaatiota kantavissa soluissa nähtiin myös liiallista replikaation aloituskohtien käyttöä, mikä viittaa replikaatiostressiin. Replikaatiostressin lisäksi PALB2-mutaation kantajasoluilla havaittiin vaikeuksia ylläpitää solusyklin G2/M-tarkastuspisteen toimintaa. Näiden solutoiminnan poikkeavuuksien takia heterotsygoottisen PALB2 c.1592delT -mutaation kantajilla todettiin genomin epävakautta ja kohonnut syöpäriski. Heterotsygoottinen ituradan mutaatio ABRAXAS-geenissä (c.1082G&#62;A) aiheuttaa dominantti-negatiivisen fenotyypin mutaation kantajasoluissa. ABRAXAS-mutaatiota kantavissa soluissa havaittiin BRCA1-proteiinitasojen laskua sekä BRCA1- ja CtIP-proteiinien vähentynyttä lokalisaatiota tumaan ja DNA-vauriopaikoille. Tämä aiheuttaa häiriöitä BRCA1-A-kompleksin paikallistumisessa, mikä johtaa häiriöihin virhealttiiden DNA-kaksoisjuoste¬katkoksien korjausmekanismien käytössä, DNA-vauriovasteessa, G2/M-tarkastus-pisteen säätelyssä ja ohjelmoidussa solukuolemassa. Tärkeimpänä löydöksenä havaittiin mutaation kantajasoluissa muuttunut transkriptioprofiili, joka johtunee BRCA1-proteiinitasojen laskusta tumassa. Näin ollen suomalainen ABRAXAS-perustajamutaatio toimii dominantti-negatiivisena BRCA1:n suhteen, aiheuttaen genomin epävakautta heterotsygoottisissa kantajasoluissa.