Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammation and subsequent destruction of synovial joints. Although its causes remain largely unknown, a substantial genetic contribution is known to exist. During the last decades the benefits of early aggressive treatment have become evident, and more potent therapeutic options have become available. These advances have increased the demands for rapid accurate diagnosis and prognostic markers of disease course and therapy response. The ‘rheumatoid factor’ (RF) has long been used as a diagnostic and prognostic marker of RA. In this thesis, the utility of measuring antibodies to cyclic citrullinated peptides (CCP) was investigated. In a population-based arthritis incidence study, 69 very early arthritis patients (symptom duration < 3 months) were identified. The anti-CCP test, performed at baseline and related to diagnosis at the 2-year follow-up, had a diagnostic specificity for RA of 96% and a sensitivity of 44%, both of which were superior to RF. In a prospective cohort of 242 incident cases of RA (symptom duration < 1 year), 64% of the patients tested positive for anti-CCP at baseline (equal to RF). Despite receiving more active anti-rheumatic therapy, the anti-CCP-positive patients had a more aggressive disease course during 3 years as compared to those testing negative. The 158VV genotype of Fcγ Receptor type IIIA (FcγRIIIA), which binds IgG with higher affinity than 158FF, was associated with an increased susceptibility to RA in men, but not in women. Previous studies report conflicting results, and none stratified according to gender. The 158V/F polymorphism of FcγRIIIA was not found to influence outcome of anti-tumour necrosis factor therapy in 282 RA patients, contradicting hints from previous studies. Genetic variation in proteins of the inflammasome, an interleukin-1 (IL-1) regulating intracellular protein complex, is associated with rare autoinflammatory conditions and possibly with Crohn’s disease. In this first study on genetic variation of the inflammasome in RA, we describe a compound polymorphism of the genes CIAS1 and TUCAN that associates both with susceptibility to RA and to the severity of the disease. Hypothetically, these genes may identify a subgroup of RA patients that would benefit from anti-IL-1 therapy. This thesis work emphasizes the benefits of testing for anti-CCP in the diagnosis and outcome prediction in early arthritis. FcγRIIIA genotype is likely to affect RA susceptibility and further work should apply a gender perspective. Inflammasome genetics may influence the risk of developing RA. Additional studies are warranted to settle whether it also identifies a subgroup of RA patients benefiting from IL-1 targeted therapy.

Li-Fraumeni Syndrome (LFS) is a rare cancer predisposition syndrome, typically involving germline mutations in the TP53 gene. Despite the high penetrance of TP53 mutations, LFS patients display striking phenotypic differences, suggesting the presence of secondary risk loci. To date, all genetic modifiers in LFS have been shown to map to either TP53 or its principal negative regulator, Mdm2. Given this strong association, we set out to interrogate the contribution of a recently-described miRNA regulator of the p53-MDM2 loop, called miR-605. We hypothesized that, if functional, the miR-605 gene and its variant (rs2043556) could impact cancer risk in TP53 mutation carriers. Consistent with this proposition, the variant allele of miR-605 was associated with a significant acceleration in tumor onset and caused a decrease in the processing efficiency of its host miRNA. We also demonstrate that miR-605 overexpression activates the MAPK pathway and leads to tumor suppression in TP53 mutant cell lines.

Li-Fraumeni Syndrome (LFS) is a rare cancer predisposition syndrome, typically involving germline mutations in the TP53 gene. Despite the high penetrance of TP53 mutations, LFS patients display striking phenotypic differences, suggesting the presence of secondary risk loci. To date, all genetic modifiers in LFS have been shown to map to either TP53 or its principal negative regulator, Mdm2. Given this strong association, we set out to interrogate the contribution of a recently-described miRNA regulator of the p53-MDM2 loop, called miR-605. We hypothesized that, if functional, the miR-605 gene and its variant (rs2043556) could impact cancer risk in TP53 mutation carriers. Consistent with this proposition, the variant allele of miR-605 was associated with a significant acceleration in tumor onset and caused a decrease in the processing efficiency of its host miRNA. We also demonstrate that miR-605 overexpression activates the MAPK pathway and leads to tumor suppression in TP53 mutant cell lines.

No description available.

Health in archaeological populations needs to be investigated using a holistic approach. Molecular techniques, particularly multiplex PCR, can be used with paleopathology and dietary analysis to understand aspects of population health. This thesis demonstrates how spina bifida, a multi-factorial disease, can be investigated using this paleoepidemiological approach. Based on skeletal evidence, spina bifida was present in a pre-Columbian Cuban population from the archaeological site of Canimar Abajo. Molecular techniques were employed to examine disease potential, examining individuals for five single nucleotide polymorphisms associated with spina bifida. It is postulated that the combined effect of these polymorphisms, as well as dietary factors, determines the risk of the population for spina bifida, and that these factors came together to create the observed high disease prevalence. Therefore, this thesis demonstrates how the methods of molecular paleopathology, corroborated by dietary analyses, can be used within a paleoepidemiological framework to understand population health and disease.

Cancer is a complex and deadly disease that is caused by genetic lesions in somatic cells. Further research in computational methodology for detecting and characterizing somatic mutations is necessary in order to understand the comprehensive systems level model of the roles of those lesions in cancer development. In the first project, I trained a list of supervised machine learning classifiers that classify false positive versus true positive somatic single nucleotide variants (SNVs). I was able to show an improvement of somatic SNV detection on the data set over the reported classifier. In the second project, we developed PhyloSub model that uses a nonparametric Bayesian prior over a set of trees to cluster SNVs, and infer the subclonal phylogenetic structure of tumors with uncertainty from SNV sequencing data. Experiments showed that PhyloSub model could infer the subclonal phylogenetic structure from both single and multiple tumor samples.

Cancer is a complex and deadly disease that is caused by genetic lesions in somatic cells. Further research in computational methodology for detecting and characterizing somatic mutations is necessary in order to understand the comprehensive systems level model of the roles of those lesions in cancer development. In the first project, I trained a list of supervised machine learning classifiers that classify false positive versus true positive somatic single nucleotide variants (SNVs). I was able to show an improvement of somatic SNV detection on the data set over the reported classifier. In the second project, we developed PhyloSub model that uses a nonparametric Bayesian prior over a set of trees to cluster SNVs, and infer the subclonal phylogenetic structure of tumors with uncertainty from SNV sequencing data. Experiments showed that PhyloSub model could infer the subclonal phylogenetic structure from both single and multiple tumor samples.

Health in archaeological populations needs to be investigated using a holistic approach. Molecular techniques, particularly multiplex PCR, can be used with paleopathology and dietary analysis to understand aspects of population health. This thesis demonstrates how spina bifida, a multi-factorial disease, can be investigated using this paleoepidemiological approach. Based on skeletal evidence, spina bifida was present in a pre-Columbian Cuban population from the archaeological site of Canimar Abajo. Molecular techniques were employed to examine disease potential, examining individuals for five single nucleotide polymorphisms associated with spina bifida. It is postulated that the combined effect of these polymorphisms, as well as dietary factors, determines the risk of the population for spina bifida, and that these factors came together to create the observed high disease prevalence. Therefore, this thesis demonstrates how the methods of molecular paleopathology, corroborated by dietary analyses, can be used within a paleoepidemiological framework to understand population health and disease.

DNA-metal ion interactions are critical for stabilizing conformations of double stranded (ds) DNA and through specific binding sites will influence the interaction of DNA with other molecules. It has been shown that different metal ions bind to different sites within nucleic acids. Work in this thesis exploits the interactions of Zn2+ with nucleic acids that are linked to surfaces. Zn2+ can interact with the phosphodiester backbone and engage in interactions with the purine nucleobases. Electrochemical studies of ds-DNA films have demonstrated that in the presence of Zn2+ films containing a single nucleotide mismatch give rise to a specific electrochemical signature. Electrochemical impedance spectroscopy (EIS) allows the discrimination of mismatched DNA films from those that are fully matched by monitoring differences in the resistance of charge transfer. Scanning electrochemical microscopy (SECM) allows multiplexing of the data acquisition and monitoring of the current response I, which is attenuated as a function of mismatch. In this thesis, various potential factors were explored in detail that may impact the discrimination of nucleotide mismatches in ds-DNA films by EIS and SECM. These factors include the position of the mismatch, its type, the number of mismatches, the length of the DNA duplex, and the length of target sequences. In particular, when the two strands are of unequal length, the resulting nucleotide overhang may mask the mismatch signature. Such overhangs are expected in real biosensor applications, in which the DNA is isolated from cellular targets. Results presented here clearly demonstrate that mismatches are readily distinguished from fully matched strands even in overhang systems, suggesting that this approach has promise for realistic sensor applications.

Diss. (sammanfattning) Uppsala : Univ., 2002. / Härtill 5 uppsatser.