Dissertations / Theses on the topic 'Molecular markers'

Using data from the China, Oxford and Virginia Commonwealth University Experimental Research on Genetic Epidemiology (CONVERGE) Consortium study of major depressive disorder (MDD)on 11,670 Han Chinese women, this thesis describes an investigation on the etiology of MDD, a psychiatric disease that has eluded previous genetic studies as well as investigations of its mechanistic underpinnings. It asks: what happens during stress, how may it contribute to the risk of developing MDD, and why does it increase the risk of MDD in some people but not others. It presents three main findings. First, a GWAS on MDD conducted on 10,640 samples (5,303 cases and 5,337 controls) in the CONVERGE dataset found two genome wide significant associations with MDD, one lying at the 5' side of SIRT1, and the other in an intron of LHPP. Both signals have been replicated in a completely independent cohort of severe MDD cases and matched controls from Northern China, making them the first replicated association loci for MDD to date. Second, I found there are more copies of mtDNA in cases of MDD than controls and while the increase can be induced by stress, it is contingent on the depressed state. Further analyses of results from animal experiments showed stress increases mtDNA levels in a dose-dependent, reversible and tissue specific way that is mediated partly by stress steroids. Third, the total amount of heteroplasmy was found to increase with increasing mtDNA levels, and therefore is higher in cases of MDD than controls, consistent with a change in mitochondrial function observed in animal models of chronic stress. All three findings suggest stress causes changes in mtDNA, and this change may be larger in cases of MDD than controls. This difference between cases and controls may be due to differences in their regulation of mtDNA levels and sequence mutation during stress, and this may be genetically determined. This study provides a new perspective to the etiology of depression, suggesting it may have origins in metabolic regulation.

Mestrado em Bioquímica - Bioquímica Clínica
Type 2 diabetes is one of the most common metabolic disorders in the world. Globally, the prevalence of this disorder is predicted to increase, along with the risk of developing diabetic related complications. One of those complications is diabetic nephropathy, defined by a progressive increase in proteinuria and a gradual decline in renal function. Approximately 25% to 30% of type 2 diabetic individuals develop this complication. However, its underlying genetic mechanisms remain unclear. Thus, the aim of this study is to contribute to the discovery of the genetic mechanisms involved in the development and progression of diabetic nephropathy, through the identification of relevant genetic variants in Portuguese type 2 diabetic individuals. The exomes of 36 Portuguese type 2 diabetic individuals were sequenced on the Ion ProtonTM Sequencer. From those individuals, 19 did not present diabetic nephropathy, being included in the control group, while the 17 individuals that presented the diabetic complication formed the case group. A statistical analysis was then performed to identify candidate common genetic variants, as well as genes accumulating rare variants that could be associated with diabetic nephropathy. From the search for common variants in the study population, the statistically significant (p-value ≤ 0.05) variants rs1051303 and rs1131620 in the LTBP4 gene, rs660339 in UCP2, rs2589156 in RPTOR, rs2304483 in the SLC12A3 gene and rs10169718 present in ARPC2, were considered as the most biologically relevant to the pathogenesis of diabetic nephropathy. The variants rs1051303 and rs1131620, as well as the variants rs660339 and rs2589156 were associated with protective effects in the development of the complication, while rs2304483 and rs10169718 were considered risk variants, being present in individuals with diagnosed diabetic nephropathy. In the rare variants approach, the genes with statistical significance (p-value ≤ 0.05) found, the STAB1 gene, accumulating 9 rare variants, and the CUX1 gene, accumulating 2 rare variants, were identified as the most relevant. Both genes were considered protective, with the accumulated rare variants mainly present in the group without the renal complication. The present study provides an initial analysis of the genetic evidence associated with the development and progression of diabetic nephropathy, and the results obtained may contribute to a deeper understanding of the genetic mechanisms associated with this diabetic complication.
A diabetes tipo 2 é um dos distúrbios metabólicos mais comuns no mundo. Globalmente, está previsto um aumento da sua prevalência, assim como um aumento do risco de desenvolver complicações associadas. Uma dessas complicações é a nefropatia diabética, definida pelo aumento progressivo de proteinúria e um declínio gradual da função renal. Aproximadamente 25% a 30% dos indivíduos com diabetes tipo 2 desenvolvem esta complicação. No entanto, os mecanismos genéticos associados permanecem por esclarecer. Posto isto, o objetivo deste estudo é contribuir para a identificação dos mecanismos envolvidos no desenvolvimento e progressão desta complicação, através da identificação de variantes genéticas relevantes, em indivíduos com diabetes tipo 2 na população portuguesa. Para isso, os exomas de 36 portugueses com diabetes tipo 2 foram sequenciados na plataforma Ion ProtonTM. Desses individuos, 19 não apresentavam nefropatia diabética, tendo sido incluídos no grupo de controlo, e os restantes 17 individuos, com a complicação diagnosticada, formaram o grupo dos casos. Uma análise estatística foi depois realizada para identificar, com base nas diferenças genéticas entre os dois grupos, variantes comuns, assim como genes que acumulam variantes raras candidatas, que podem explicar o risco acrescido ou diminuído para desenvolver a complicação. Na pesquisa das variantes comuns, as variantes rs1051303 e o rs1131620 no gene LTBP4, a variante rs660339 no UCP2, a variante rs2589156 no gene RPTOR, a variante rs2304483 no SLC12A3 e, por fim, a variante rs10169718 presente no gene ARPC2, foram, de todas aquelas consideradas estatisticamente significativas (p-value ≤ 0,05), as mais relevantes para a patogénese da nefropatia diabética. O rs1051303 e o rs1131620, assim como o rs660339 e o rs2589156, têm um efeito protetor, enquanto o rs2304483 e o rs10169718 foram considerados de risco, estando associados a indivíduos que sofrem da complicação referida. Pela abordagem utilizada para identificar as variantes raras, o gene STAB1, que acumula 9 variantes, e o gene CUX1, que acumula 2, foram, de todos os genes com significado estatístico (p-value ≤ 0,05), aqueles que se evidenciaram como sendo biologicamente relevantes. Ambos os genes foram considerados protetores, já que as suas variantes raras acumuladas estavam presentes maioritariamente nos indivíduos que não apresentam esta complicação renal. Este estudo providencia uma análise inicial das evidências genéticas associadas ao desenvolvimento e progressão da nefropatia diabética, podendo os seus reultados contribuir para uma melhor compreensão dos mecanismos genéticos que estão por detrás do seu surgimento.

Recently it has been shown that the consumption of a diet high in saturated fat is associated with impaired insulin sensitivity and increased incidence of type 2 diabetes. In contrast, diets that are high in monounsaturated fatty acids (MUFAs) or polyunsaturated fatty acids (PUFAs), especially very long chain n-3 fatty acids (FAs), are protective against disease. However, the molecular mechanisms by which saturated FAs induce the insulin resistance and hyperglycaemia associated with metabolic syndrome and type 2 diabetes are not clearly defined. It is possible that saturated FAs may act through alternative mechanisms compared to MUFA and PUFA to regulate of hepatic gene expression and metabolism. It is proposed that, like MUFA and PUFA, saturated FAs regulate the transcription of target genes. To test this hypothesis, hepatic gene expression analysis was undertaken in a human hepatoma cell line, Huh-7, after exposure to the saturated FA, palmitate. These experiments showed that palmitate is an effective regulator of gene expression for a wide variety of genes. A total of 162 genes were differentially expressed in response to palmitate. These changes not only affected the expression of genes related to nutrient transport and metabolism, they also extend to other cellular functions including, cytoskeletal architecture, cell growth, protein synthesis and oxidative stress response. In addition, this thesis has shown that palmitate exposure altered the expression patterns of several genes that have previously been identified in the literature as markers of risk of disease development, including CVD, hypertension, obesity and type 2 diabetes. The altered gene expression patterns associated with an increased risk of disease include apolipoprotein-B100 (apo-B100), apo-CIII, plasminogen activator inhibitor 1, insulin-like growth factor-I and insulin-like growth factor binding protein 3. This thesis reports the first observation that palmitate directly signals in cultured human hepatocytes to regulate expression of genes involved in energy metabolism as well as other important genes. Prolonged exposure to long-chain saturated FAs reduces glucose phosphorylation and glycogen synthesis in the liver. Decreased glucose metabolism leads to elevated rates of lipolysis, resulting in increased release of free FAs. Free FAs have a negative effect on insulin action on the liver, which in turn results in increased gluconeogenesis and systemic dyslipidaemia. It has been postulated that disruption of glucose transport and insulin secretion by prolonged excessive FA availability might be a non-genetic factor that has contributed to the staggering rise in prevalence of type 2 diabetes. As glucokinase (GK) is a key regulatory enzyme of hepatic glucose metabolism, changes in its activity may alter flux through the glycolytic and de novo lipogenic pathways and result in hyperglycaemia and ultimately insulin resistance. This thesis investigated the effects of saturated FA on the promoter activity of the glycolytic enzyme, GK, and various transcription factors that may influence the regulation of GK gene expression. These experiments have shown that the saturated FA, palmitate, is capable of decreasing GK promoter activity. In addition, quantitative real-time PCR has shown that palmitate incubation may also regulate GK gene expression through a known FA sensitive transcription factor, sterol regulatory element binding protein-1c (SREBP-1c), which upregulates GK transcription. To parallel the investigations into the mechanisms of FA molecular signalling, further studies of the effect of FAs on metabolic pathway flux were performed. Although certain FAs reduce SREBP-1c transcription in vitro, it is unclear whether this will result in decreased GK activity in vivo where positive effectors of SREBP-1c such as insulin are also present. Under these conditions, it is uncertain if the inhibitory effects of FAs would be overcome by insulin. The effects of a combination of FAs, insulin and glucose on glucose phosphorylation and metabolism in cultured primary rat hepatocytes at concentrations that mimic those in the portal circulation after a meal was examined. It was found that total GK activity was unaffected by an increased concentration of insulin, but palmitate and eicosapentaenoic acid significantly lowered total GK activity in the presence of insulin. Despite the fact that total GK enzyme activity was reduced in response to FA incubation, GK enzyme translocation from the inactive, nuclear bound, to active, cytoplasmic state was unaffected. Interestingly, none of the FAs tested inhibited glucose phosphorylation or the rate of glycolysis when insulin is present. These results suggest that in the presence of insulin the levels of the active, unbound cytoplasmic GK are sufficient to buffer a slight decrease in GK enzyme activity and decreased promoter activity caused by FA exposure. Although a high fat diet has been associated with impaired hepatic glucose metabolism, there is no evidence from this thesis that FAs themselves directly modulate flux through the glycolytic pathway in isolated primary hepatocytes when insulin is also present. Therefore, although FA affected expression of a wide range of genes, including GK, this did not affect glycolytic flux in the presence of insulin. However, it may be possible that a saturated FA-induced decrease in GK enzyme activity when combined with the onset of insulin resistance may promote the dys-regulation of glucose homeostasis and the subsequent development of hyperglycaemia, metabolic syndrome and type 2 diabetes.

Thesis (MSc)--Stellenbosch University, 2012.
Triticale is an amphidiploid that consists of wheat (A and B) and rye (R) genomes. This cereal is fast becoming important on a commercial basis and warrants further assessment for the better management and breeding of the hybrid. The assessment of the genetic diversity among the wheat and rye genomes within triticale can be obtained by using molecular markers developed in both donor genomes. Simple sequence repeats markers (SSRs) and amplified fragment length markers (AFLPs) have been previously used to assess the genetic diversity among triticale lines. SSRs are highly polymorphic markers that are abundant and which have been shown to be highly transferable between species in previous studies while AFLP markers are known to generate plenty of data as they cover so many loci. Thus, the aim of this study was to develop a marker system suitable to assess the genetic diversity and relationships of advanced breeding material (and cultivars) of the Stellenbosch University’s Plant Breeding Laboratory (SU-PBL). Therefore, both AFLP and SSR markers were initially analysed using eight triticale cultivars (with known pedigrees) to facilitate cultivar identification. Fourty-two AFLP primer combinations and 86 SSR markers were used to assess the genetic diversity among the Elite triticale cultivars. The AFLP primer combinations generated under average polymorphism information content (PIC) values. Furthermore, these markers generated neighbour-joining (NJ) and unweighted pair group method with arithmetic average (UPGMA) dendograms that displayed relationships that did not correspond with the available pedigree information. Therefore, this marker system was found not to be suitable. A set of 86 SSRs previously identified in both wheat and rye, was used to test the genetic diversity among the eight cultivars. The markers developed in wheat achieved 84% transferability while those developed in rye achieved 79.3% transferability. A subset of SSR markers was able to distinguish the cultivars, and correctly identify them by generating NJ and UPGMA dendograms that exhibited relationships that corroborated the available pedigree data. This panel of markers was therefore chosen as the most suitable for the assessment of the advanced breeding material. The panel of seven SSR markers was optimised for semi-automated analysis and was used to screen and detect the genetic diversity among 306 triticale entries in the F6, Senior and Elite phases of the SU-PBL triticale breeding programme. An average PIC value of 0.65 was detected and moderate genetic variation was observed. NJ and UPGMA dendograms generated showed no clear groupings. However, the panel of markers managed to accurately identify all cultivars within the breeding program. The marker panel developed in this study is being used to routinely distinguish among the advanced breeding material within the SU-PBL triticale breeding programme and as a tool in molecular-assisted backcross.

Renal cell carcinoma (RCC) is the most deadly of urological malignancies. While metastatic disease affects one third of patients at diagnosis, a further third of patients who undergo extirpative surgery with curative intent subsequently develop metastatic disease. Inconsistency in the clinical course ensures predicting subsequent metastasis is notoriously difficult, despite the routine use of prognostic clinico-pathological parameters in risk stratification. With greater understanding of pathways involved in disease pathogenesis, a number of biomarkers have been proposed to be of prognostic significance; however there are currently no molecular prognostic markers in clinical use. Genetic intra-tumoural heterogeneity (genetic ITH) has been described in clear cell RCC (ccRCC) and may limit the clinical translation of biomarkers. There has been no assessment of ITH at other molecular levels. The aim of this work was to define and compare proteomic, transcriptomic and DNA methylation ITH in ccRCC, and identify potential prognostic biomarkers. Using reverse phase protein arrays to study protein expression in multiple spatially separate regions of primary and metastatic ccRCC, proteomic ITH was demonstrated for the first time. Interestingly there was no significant difference in proteomic ITH in metastatic ccRCC tumour deposits compared to primary tumours. However, on analysis of differential protein expression between primary and metastatic ccRCC tissue using a tissue microarray and automated analysis of immunofluorescence, there was significantly greater expression of Ki67, p53, VEGFR1, SLUG and SNAIL in the metastases compared to the primary tumours. Subsequent profiling of gene expression and DNA methylation in multiple areas of the same primary tumours confirmed transcriptomic and methylomic ITH. On comparison of this multimolecular ITH, significantly greater proteomic ITH was seen compared to gene expression and DNA promoter methylation heterogeneity. Recent evidence suggests DNA methylation may be prognostically important in RCC and given the lower methylomic ITH in ccRCC, the identification of prognostic DNA methylation changes in ccRCC were pursued using the Infinium HumanMethylation450K Beadchip. Following development of an analysis pipeline, identification and validation of prognostic differentially methylated regions (DMR) was performed on an experimental cohort and published dataset respectively. Five DMRs, which were associated with disease recurrence in ccRCC, were identified. NEFM gene promoter methylation was the only DMR associated with cancer specific survival, independent of TNM stage and nuclear grade on multivariate analysis, which was confirmed on a third independent published dataset. This thesis therefore demonstrates multi-molecular ITH in ccRCC for the first time. Despite this, NEFM promoter methylation may be a useful independent prognostic marker of cancer specific survival.

Abstract Loss of insulin-producing β-cells is central to the development of Type 1 diabetes (T1D). Currently, we lack diagnostic tools to quantitate this β-cell loss. Non-protein coding RNAs called microRNAs (miRNAs/miRs) play an important role in islet development and function. Recent detection of miRNAs in peripheral circulation, has renewed interest in microRNA biomarkers of diabetes. Comparably, circulating insulin cell-free (cf)DNA has been proposed as a direct biomarker of β-cell death. DNA methylation studies have identified specific sites within DNA that are unmethylated in β-cells but methylated in other cell types, thus providing a handle to discriminate between cfDNA from β-/non-β-cells. Previous research carried out in the Hardikar lab identified a signature of 20 miRNAs (the ‘RAPID’ signature) with potential as a biomarker of β-cell death. The RAPID signature was revised to accommodate other microRNAs finally constituting a panel of 50 microRNAs (PREDICT T1D panel). An analysis of these 50 miRNAs, as well as insulin cfDNA in serum/plasma from individuals before, during and after clinical diagnosis of T1D is presented. Human islet cell death assays using sodium nitroprusside exposure identified a subset of 27 miRNAs and insulin cfDNA associated with islet cell stress/death. Non-obese diabetic mice (N=32) were found to have elevated candidate miRNAs prior to immune infiltration and glycaemic dysfunction. This trend was also noted in the human progression to T1D; 26 miRNAs were elevated in (N=19) high-risk individuals and those at diagnosis (N=199) but decreased within 6-weeks after diagnosis. Furthermore, candidate miRNAs exhibited differential abundance with disease duration, residual C-peptide, and microvascular complications in 180 subjects with prolonged T1D. At diagnosis, miRNAs and cfDNA associated with GAD III autoantibody titres (N=167 P-values range from 0.044 to <0.0001) and HbA1c levels (N=187, P-values range from 0.047 to 0.00095). Such biomarkers may inform medical researchers as to how to predict the development of T1D, monitor response to interventions such as islet transplantation, vaccines & drugs aiming to retard β-cell loss. In basic research, such an assay may help to select treatments to block β-cell death and guide the development of new treatments to lessen the burden of diabetes.

Previous studies of molecular prognostic markers following resection for exocrine pancreatic cancer have produced conflicting results. The aim of this study was to undertake a comprehensive analysis of potentially useful markers in a large multicentre patient population and compare these markers with standard pathological prognostic variables. Formalin fixed, paraffin-embedded specimens of pancreatic ductal adenocarcinoma were analysed from 157 patients (100 men and 57 women with a median [range] age of 60 [33-77] years) who had undergone pancreatectomy. Immunhistochemistry was used to detect expression of p16\(^{INK4}\), p53, p21\(^{WAF1}\), cyclin D1, c-erbB-2 and c-erbB-3. In a selected number of p53 positive and negative staining cases, mutational analysis was undertaken using DNA obtained from microdissected specimens. Mutations in codons 12 and 13 of the K-ras oncogene were detected by SSCP and sequencing following DNA extraction and amplification by PCR. The median [range] survival post-resection was 12.5 [3-83] months. Abnormalities of p16\(^{INK4}\), p53, p21\(^{WAF1}\), cyclin D1, c-erbB-2 and c-erbB-3 expression were found in 87%, 41%, 75%, 72%, 33% and 57% of cases, respectively. There was no significant correlation between expression of any of these markers and patient survival. K-ras mutations were found in 73 (75%) out of 97% cases with amplifiable DNA. The presence of K-ras mutation alone did not correlate with survival, but there were significant differences in survival according to the type of K-ras mutation (p=0.0007). Reduced survival was found in patients with GaT, cGT and GcT K-ras mutations compared to GtT, aGT and GaC mutations. In conclusion survival was associated with the type of K-ras mutation but not the expression of p16\(^{INK4}\), p53, p21\(^{WAF1}\), cyclinD1, c-erbB-2 and c-erbB3.

Mefenoxam has been a premier compound for Phytophthora disease control in the nursery industry for 30 years. The primary objectives of this research were to examine whether Phytophthora species have developed resistance to this compound and to investigate fungicide resistance management strategies. Phytophthora nicotianae, a destructive pathogen of numerous herbaceous and some woody ornamental plants, was used as a model system. P. cinnamomi, a major pathogen of a wide range of tree species and shrub plants, was also included for comparison. Twenty-six isolates of P. nicotianae were highly resistant to mefenoxam with a mean EC50 value of 326.5 µg/ml while the remaining 70 were sensitive with an EC50 of <0.01 µg/ml (Label rate: 0.08µg/ml). All resistant isolates were recovered from herbaceous annuals and irrigation water in 3 Virginia nurseries. Resistant isolates were compared with sensitive ones using seedlings of Lupinus â Russell Hybridsâ in the absence of mefenoxam for relative competitive ability. Resistant isolates out-competed sensitive ones within 3 to 6 sporulation cycles. Resistant isolates exhibited greater infection rate and higher sporulation ability than sensitive ones. No mefenoxam resistant isolates were identified in P. cinnamomi. All 65 isolates of P. cinnamomi were sensitive to mefenoxam with an EC50 of < 0.04 ï ­g/ml. Attempts to generate mutants with high resistance to mefenoxam through UV mutagenesis and mycelial adaptation were not successful. However, there were significant reductions in sensitivity to mefenoxam; those slightly resistant mutants carried fitness penalties, which may explain why P. cinnamomi remains sensitive to mefenoxam. The effect of propamocarb hydrochloride on different growth stages of Phytophthora nicotianae was evaluated in search for an alternative fungicide. Propamocarb greatly inhibited sporangium production, zoospore motility, germination and infection. However, it has little inhibition of mycelial growth and infections. Propamocarb can be used as an alternative fungicide to mefenoxam where mefenoxam resistance has become problematic. However, it must be used preventively; i.e. before infections occur. The genetic inheritance of mefenoxam resistance in P. nicotianae was studied using F1 progenies of a cross between resistant and sensitive isolates. The F1 progenies segregated for mefenoxam resistance in ratio of 1R:1S, indicating the mefenoxam resistance is controlled by a single dominant gene. One RAPD marker putatively linked to resistant locus in repulsion phase was obtained by bulked segregant analysis and was converted to the SCAR marker. This marker is capable of differentiating mefenoxam resistant populations from sensitive populations included in this study.
Ph. D.

In this study different molecular techniques are contrasted (RAPD's, allozyme, sequencing mtDNA, sequencing ribosomal spacers) and appropriate analytical methods (allelic and infinite-sites approaches; inbreeding and coalescent models) used for estimating population genetic parameters in parasites. A range of population genetic questions at different scales were chosen to emphasise the importance of tailoring techniques and analytical methods to the particular question being investigated. The realisation that each question formulated has a particular scale means the appropriate technique and markers must be useful at that scale to attempt to answer the question. The useful scale of a technique depends several factors including the region of DNA examined, the density of sampling of the technique, and the mode of evolution of the markers. Each technique will produce a useful range of variability. Below the lower limit there is no variation, above the upper limit the variation is too high to produce useful comparisons. Parasites are of interest for many reasons, primarily because they can cause disease and thus impact on their host's population dynamics. They are often closely associated with their hosts and may undergo co-evolution, as well as causing an ongoing immunological "arms race" with their hosts. The parasitic mode of live is found throughout nearly all taxonomic groupings and thus classical models of population genetics based on sexual, diploid vertebrates do not fit well with the entire diversity of parasite groups. Genetic diversity within and among populations of Echinococcus granulosus was examined contrasting a RAPD dataset with an allozyme dataset. Two models of variation in Echinococcus have been proposed, those of Smyth and Rausch, and the expected genetic structure from each was compared to the observed genetic structure. The premise of Smyth’s model, predominant self-fertilisation, was supported, but the resultant pattern of genetic variation followed Rausch’s model. RAPD data, being dominant, present challenges to analysis. An approach to overcome this dominance problem and allow standard allelic frequency analysis is described using the selfing rate estimated from allozyme data. The RAPD data were also analysed using both band-sharing and nucleotide diversity approaches. A population genetic study of Ostertagia ostertagi in the USA was extended to two different scales: within an Australian state and between the USA and Australian continents. Three alternative explanations for the observed discrepancy between genetic structure and differentiation in an important biological trait, hypobiosis, were explored. A number of programs and analyses were compared including coalescent geneflow estimates. Variation among multiple copies of two spacer regions of rDNA was examined within individuals of Ostertagia ostertagi. Both the intergenic spacer and internal transcribed spacer 1 regions were found to include repeat regions, with different numbers of repeats creating length differences in clones from the same worm. Multi-copy genes present extra challenges in analysis to ensure that only homologous copies are being compared. Many studies fail to look for variation within populations or within individuals. The two major conclusions from these examples are that: 1). The study of variation necessarily involves an implicit scale, and markers must be chosen that are appropriate to the question being explored. 2). Using several methods of analysis of genetic data allows contrasts to be made, and if different methods produce similar results gives much more confidence in the conclusions drawn. Incongruence in results leads to new questions and reexamination of the assumptions of each analysis.

In this study different molecular techniques are contrasted (RAPD's, allozyme, sequencing mtDNA, sequencing ribosomal spacers) and appropriate analytical methods (allelic and infinite-sites approaches; inbreeding and coalescent models) used for estimating population genetic parameters in parasites. A range of population genetic questions at different scales were chosen to emphasise the importance of tailoring techniques and analytical methods to the particular question being investigated. The realisation that each question formulated has a particular scale means the appropriate technique and markers must be useful at that scale to attempt to answer the question. The useful scale of a technique depends several factors including the region of DNA examined, the density of sampling of the technique, and the mode of evolution of the markers. Each technique will produce a useful range of variability. Below the lower limit there is no variation, above the upper limit the variation is too high to produce useful comparisons. Parasites are of interest for many reasons, primarily because they can cause disease and thus impact on their host's population dynamics. They are often closely associated with their hosts and may undergo co-evolution, as well as causing an ongoing immunological "arms race" with their hosts. The parasitic mode of live is found throughout nearly all taxonomic groupings and thus classical models of population genetics based on sexual, diploid vertebrates do not fit well with the entire diversity of parasite groups. Genetic diversity within and among populations of Echinococcus granulosus was examined contrasting a RAPD dataset with an allozyme dataset. Two models of variation in Echinococcus have been proposed, those of Smyth and Rausch, and the expected genetic structure from each was compared to the observed genetic structure. The premise of Smyth's model, predominant self-fertilisation, was supported, but the resultant pattern of genetic variation followed Rausch's model. RAPD data, being dominant, present challenges to analysis. An approach to overcome this dominance problem and allow standard allelic frequency analysis is described using the selfing rate estimated from allozyme data. The RAPD data were also analysed using both band-sharing and nucleotide diversity approaches. A population genetic study of Ostertagia ostertagi in the USA was extended to two different scales: within an Australian state and between the USA and Australian continents. Three alternative explanations for the observed discrepancy between genetic structure and differentiation in an important biological trait, hypobiosis, were explored. A number of programs and analyses were compared including coalescent geneflow estimates. Variation among multiple copies of two spacer regions of rDNA was examined within individuals of Ostertagia ostertagi. Both the intergenic spacer and internal transcribed spacer 1 regions were found to include repeat regions, with different numbers of repeats creating length differences in clones from the same worm. Multi-copy genes present extra challenges in analysis to ensure that only homologous copies are being compared. Many studies fail to look for variation within populations or within individuals. The two major conclusions from these examples are that: 1). The study of variation necessarily involves an implicit scale, and markers must be chosen that are appropriate to the question being explored. 2). Using several methods of analysis of genetic data allows contrasts to be made, and if different methods produce similar results gives much more confidence in the conclusions drawn. Incongruence in results leads to new questions and reexamination of the assumptions of each analysis.

The use of organs from donors after circulatory death (DCD) has been recommended as one strategy to enlarge the donor pool and raise the transplant rate. However, DCD allografts had higher incidence of early post-transplant dysfunction. The general aim of this research project was to develop clinical and experimental strategies to reduce the incidence of early post-transplant dysfunction of kidney and liver allografts from DCD. First the ability of a clinical scoring system based on donor data for identifying DCD kidneys with high-risk of post-transplant dysfunction was evaluated using the Oxford and the UK National DCD kidney transplant cohorts. This works suggest that stratification of DCD kidneys before transplantation might allow early identification of kidneys in which lower graft function and survival could be expected if any additional therapeutic intervention is implemented. Second, as it has been suggested that hypothermic machine perfusion (HMP) may protect DCD kidneys from additional preservation injury and improve their outcome after transplantation, this work explored the benefit of HMP as preservation technique fo DCD kidneys in Oxford and discusses the potential of this technique for reducing the incidence of post-transplant dysfunction in DCD kidneys. The Oxford. Liver Group has provided evidence of the benefit of preservation with normothermic machine perfusion (NMP) on post-transplant function and survival of DCD liver allografts. In this work, the molecular mechanisms associated with this benefit were characterized using micro array technology. This analysis suggests that the beneficial effect ofNMP may be associated with the induction of the ischaemic preconditioning phenomenon and highlights a group of genes with potential for gene therapy. Finally, this works provides the "proof-of-concept" that the use of a non-mammalian viral vector for gene transfer of kidneys and livers during conventional cold preservation is feasible and is not associated with additional tissue injury.

In vitro fertilization treatments are responsible for 1-5% births in industrialized countries. The safest way to generate a pregnancy is to transfer a single embryo to the mother, reducing the likelihood of multiple gestations. Hence, in order to maximize the chance of success, it is extremely important that the embryo prioritised for transfer is the most capable within the cohort of embryos generated by the patient. Along with cytogenetic components, it has been suggested that embryo protein expression patterns may correlate with its ability to implant. However, embryo proteomics strategies have not been easy to harness mainly due to the complexity of the media the embryos are cultured in, and the low concentration of the proteins that are secreted. In this study, the use of the blastocentesis procedure, which allows the safe retrieval of embryo inner fluid (blastosol), was described. The use of the blasocoel fluid as a source of embryonic DNA for preimplantation genetic assessment was also investigated. From this highly purified embryonic sample, a comprehensive catalogue of proteins present in the human blastosol was generated using standard and custom- made mass spectrometry strategies. The embryonic origin of these proteins was validated by gene expression microarray and RNASeq analysis. These experiments also allowed the identification of differentially expressed genes in the first two cell lineages, the Inner Cell Mass and the Trophectoderm. Finally, a targeted proteomics strategy able to measure part of the previously described protein targets in single blastosol samples was employed. The correlation between the presence and abundance of proteins of interest in single blastosols and several biological characteristics of the embryo, including its chromosomal status, was assessed. These data are of major interest for the understanding of human embryo development. The validated embryo-derived protein catalogue and blastocyst gene expression profiles generated in this study, provides access to a thorough document for consultation in human embryology proteomics-based experiment design, paving the way to next-generation proteomic-based embryo assessment.

In this study different molecular techniques are contrasted (RAPD's, allozyme, sequencing mtDNA, sequencing ribosomal spacers) and appropriate analytical methods (allelic and infinite-sites approaches; inbreeding and coalescent models) used for estimating population genetic parameters in parasites. A range of population genetic questions at different scales were chosen to emphasise the importance of tailoring techniques and analytical methods to the particular question being investigated. The realisation that each question formulated has a particular scale means the appropriate technique and markers must be useful at that scale to attempt to answer the question. The useful scale of a technique depends several factors including the region of DNA examined, the density of sampling of the technique, and the mode of evolution of the markers. Each technique will produce a useful range of variability. Below the lower limit there is no variation, above the upper limit the variation is too high to produce useful comparisons. Parasites are of interest for many reasons, primarily because they can cause disease and thus impact on their host's population dynamics. They are often closely associated with their hosts and may undergo co-evolution, as well as causing an ongoing immunological "arms race" with their hosts. The parasitic mode of live is found throughout nearly all taxonomic groupings and thus classical models of population genetics based on sexual, diploid vertebrates do not fit well with the entire diversity of parasite groups. Genetic diversity within and among populations of Echinococcus granulosus was examined contrasting a RAPD dataset with an allozyme dataset. Two models of variation in Echinococcus have been proposed, those of Smyth and Rausch, and the expected genetic structure from each was compared to the observed genetic structure. The premise of Smyth's model, predominant self-fertilisation, was supported, but the resultant pattern of genetic variation followed Rausch's model. RAPD data, being dominant, present challenges to analysis. An approach to overcome this dominance problem and allow standard allelic frequency analysis is described using the selfing rate estimated from allozyme data. The RAPD data were also analysed using both band-sharing and nucleotide diversity approaches. A population genetic study of Ostertagia ostertagi in the USA was extended to two different scales: within an Australian state and between the USA and Australian continents. Three alternative explanations for the observed discrepancy between genetic structure and differentiation in an important biological trait, hypobiosis, were explored. A number of programs and analyses were compared including coalescent geneflow estimates. Variation among multiple copies of two spacer regions of rDNA was examined within individuals of Ostertagia ostertagi. Both the intergenic spacer and internal transcribed spacer 1 regions were found to include repeat regions, with different numbers of repeats creating length differences in clones from the same worm. Multi-copy genes present extra challenges in analysis to ensure that only homologous copies are being compared. Many studies fail to look for variation within populations or within individuals. The two major conclusions from these examples are that: 1). The study of variation necessarily involves an implicit scale, and markers must be chosen that are appropriate to the question being explored. 2). Using several methods of analysis of genetic data allows contrasts to be made, and if different methods produce similar results gives much more confidence in the conclusions drawn. Incongruence in results leads to new questions and reexamination of the assumptions of each analysis.

Traditional morphological examinations are not anymore sufficient for a complete evaluation of tumoral tissue and the use of neoplastic markers is of utmost importance. Neoplastic markers can be classified in: diagnostic, prognostic and predictive markers. Three markers were analyzed. 1) Insulin-like growth factor binding protein 2 (IGFBP2) was immunohistochemically examined in prostatic tissues: 40 radical prostatectomies from hormonally untreated patients with their preoperative biopsies, 10 radical prostatectomies from patients under complete androgen ablation before surgery and 10 simple prostatectomies from patients with bladder outlet obstruction. Results were compared with α-methylacyl-CoA racemase (AMACR). IGFBP2 was expressed in the cytoplasm of untreated adenocarcinomas and, to a lesser extent, in HG-PIN; the expression was markedly lower in patients after complete androgen ablation. AMACR was similarly expressed in both adenocarcinoma and HG-PIN, the level being similar in both lesions; the expression was slightly lower in patients after complete androgen ablation. IGFBP2 may be used a diagnostic marker of prostatic adenocarcinomas. 2) Heparan surface proteoglycan immunohistochemical expression was examined in 150 oral squamous cell carcinomas. Follow up information was available in 93 patients (range: 6-34 months, mean: 19±7). After surgery, chemotherapy was performed in 8 patients and radiotherapy in 61 patients. Multivariate and univariate overall survival analyses showed that high expression of syndecan-1 (SYN-1) was associated with a poor prognosis. In patients treated with radiotherapy, such association was higher. SYN-1 is a prognostic marker in oral squamous cell carcinomas; it may also represent a predictive factor for responsiveness to radiotherapy. 3) EGFR was studied in 33 pulmonary adenocarcinomas with traditional DNA sequencing methods and with two mutation-specific antibodies. Overall, the two antibodies had 61.1% sensitivity and 100% specificity in detecting EGFR mutations. EGFR mutation-specific antibodies may represent a predictive marker to identify patients candidate to tyrosine kinase inhibitors therapy.

Traditional morphological examinations are not anymore sufficient for a complete evaluation of tumoral tissue and the use of neoplastic markers is of utmost importance. Neoplastic markers can be classified in: diagnostic, prognostic and predictive markers. Three markers were analyzed. 1) Insulin-like growth factor binding protein 2 (IGFBP2) was immunohistochemically examined in prostatic tissues: 40 radical prostatectomies from hormonally untreated patients with their preoperative biopsies, 10 radical prostatectomies from patients under complete androgen ablation before surgery and 10 simple prostatectomies from patients with bladder outlet obstruction. Results were compared with α-methylacyl-CoA racemase (AMACR). IGFBP2 was expressed in the cytoplasm of untreated adenocarcinomas and, to a lesser extent, in HG-PIN; the expression was markedly lower in patients after complete androgen ablation. AMACR was similarly expressed in both adenocarcinoma and HG-PIN, the level being similar in both lesions; the expression was slightly lower in patients after complete androgen ablation. IGFBP2 may be used a diagnostic marker of prostatic adenocarcinomas. 2) Heparan surface proteoglycan immunohistochemical expression was examined in 150 oral squamous cell carcinomas. Follow up information was available in 93 patients (range: 6-34 months, mean: 19±7). After surgery, chemotherapy was performed in 8 patients and radiotherapy in 61 patients. Multivariate and univariate overall survival analyses showed that high expression of syndecan-1 (SYN-1) was associated with a poor prognosis. In patients treated with radiotherapy, such association was higher. SYN-1 is a prognostic marker in oral squamous cell carcinomas; it may also represent a predictive factor for responsiveness to radiotherapy. 3) EGFR was studied in 33 pulmonary adenocarcinomas with traditional DNA sequencing methods and with two mutation-specific antibodies. Overall, the two antibodies had 61.1% sensitivity and 100% specificity in detecting EGFR mutations. EGFR mutation-specific antibodies may represent a predictive marker to identify patients candidate to tyrosine kinase inhibitors therapy.

Due to their capital diagnostic, prognostic and therapeutic implications, molecular markers have become essential for the management of patients with diffuse gliomas. Among them, IDH mutations have special importance, as they allow to classify diffuse gliomas, they are predictive of prolonged survival and increased sensitivity to alkylating agents and can be targeted by specific inhibitors. IDH-mutant diffuse gliomas deeply differ from IDH-wildtype diffuse gliomas in terms of molecular profile, prognosis and treatment, as different are the pathways of gliomagenesis and progression in the two groups. In the first section of the thesis, we explored the association between 25 glioma risk loci and tumor genotype in a large cohort of glioma patients for whom we disposed of both germline and tumor DNA. Our study confirmed that IDH-mutant and IDH-wildtype gliomas are associated with different susceptibility loci and that certain germline risk loci associate with distinct molecular groups, suggesting a direct involvement in their pathogenesis. In the second section of the thesis, we assessed the performance of two different techniques for the noninvasive detection of IDH mutations. The first technique is based on the identification of IDH1 mutations from the analysis of tumor-derived extracellular vesicles circulating in plasma, a procedure generally referred to as “liquid biopsy”. The second technique is based on the detection of 2-hydroxyglutarate, a metabolite that reflects the presence of IDH mutations, using in vivo magnetic resonance spectroscopy. While the experiments of liquid biopsy posed major challenges due to the limited amount of tumor-derived material circulating in plasma, magnetic resonance spectroscopy proved an overly sensitive and specific technique for the diagnosis and follow-up of patients with IDH-mutant gliomas. In the third section of the thesis, we focused on three rare subsets of IDH-wildtype gliomas with the aim to better characterize their genetic profile, define their prognosis, and assess the prevalence of actionable alterations. We identified different mutational and immunological signatures in high- and low-grade gliomas associated with type 1 neurofibromatosis, we identified recurrent FGFR1 mutations in midline gliomas and frequent FGFR3-TACC3 fusions in low-grade astrocytomas lacking IDH mutations, observations that pave the way to the experimentation of novel therapeutic approaches for these rare tumor types. In the fourth and last section of the thesis, we analyzed the response to targeted treatment in a cohort of adult patients with recurrent or disseminated BRAF-mutant gliomas. The substantial response rate observed in our study encourages the use of RAF/MEK inhibitors in BRAF-mutant gliomas and emphasizes the importance of screening for this rare but actionable alteration.

Introduzione. I cordomi della base cranica sono tumori rari e a lenta crescita derivanti dalla notocorda. La loro morbilità è principalmente legata alla loro invasione locale e alla resistenza ai trattamenti. A causa del loro aspetto eterogeneo e del loro comportamento clinico-molecolare non completamente compreso, l'obiettivo principale del presente lavoro è quello di identificare marcatori clinici e bio-molecolari come fattori prognostici specifici che potrebbero essere utilizzati per la corretta gestione di tali pazienti. Il raggiungimento di una firma prognostica dettagliata dei cordomi del basicranio è di fondamentale importanza per poter personalizzare il trattamento di ciascun paziente. Inoltre, l'analisi degli sfingolipidi sta emergendo come un nuovo approccio in molti tumori e non è mai stata applicata nei cordomi. L’obiettivo principale è lo studio del comportamento biologico del cordoma e il ruolo della produzione di ceramidi in questo contesto di proliferazione e invasione locale. Pazienti e Metodi. È stata eseguita una revisione retrospettiva di tutti i pazienti diagnosticati e trattati per cordoma della base cranica presso la Fondazione IRCCS Istituto Neurologico "Carlo Besta" tra il gennaio 1992 ed il dicembre 2017. Sono stati raccolti dati clinici, radiologici, chirurgici e patologici. È stata eseguita una raccolta prospettica di campioni chirurgici congelati per analizzare le specie di ceramidi. Gli sfingolipidi sono stati estratti dai tessuti congelati; i ceramidi e i diidroceramidi sono stati valutati mediante cromatografia liquida e spettrometria di massa. L'analisi di sopravvivenza è stata eseguita secondo il metodo di Kaplan-Meier. I confronti univariati sono stati condotti usando i test di Mann-Whitney, Chi-square e il test esatto di Fisher. Sono state condotte analisi di regressione e correlazione lineari. Utilizzando un modello di regressione logistica, i predittori statisticamente significativi sono stati pesati sulla base dei loro odds ratio al fine di sviluppare una scala personalizzata - la Peri-Operative Chordoma Scale (POCS). Risultati. Ottantasette pazienti sono stati trattati chirurgicamente per cordoma del basicranio. Settantotto pazienti sono stati dichiarati eleggibili per la revisione. I pazienti erano 38 maschi (48.7%) e 40 femmine (51.3%). Il follow-up medio era di 69 mesi (intervallo, 3-233). Sono stati eseguiti centoquattordici interventi chirurgici. La presenza di deficit motori si è rivelata essere un fattore prognostico significativo correlato a una PFS peggiore (p=0.0480). La presenza di calcificazioni ha mostrato una correlazione con risultati migliori di OS rispetto al tumore privo di calcificazioni (p=0.0420). Il grado di impregnazione contrastografica alla RM si è rivelato essere un fattore prognostico significativo in termini sia di OS che di PFS (p≤0.0001 e 0.0010, rispettivamente). Il coinvolgimento del forame giugulare e delle cisterne anteriori al tronco encefalico si sono rivelati due fattori prognostici significativi correlati con una riduzione di PFS (p=0.0130 e p=0.0210, rispettivamente). La dislocazione del tronco cerebrale rappresentava un fattore prognostico significativo correlato a peggiore OS e PFS nella coorte di cordomi recidivi (p=0.0060 e 0.0030, rispettivamente). L'estensione della resezione tumorale rappresentava un forte fattore prognostico secondo la PFS nella coorte di cordomi primari (p=0.0200). I pazienti operati da un chirurgo esperto (definito come il chirurgo che ha eseguito più di 10 procedure chirurgiche per cordoma del basicranio nella presente serie) hanno avuto un outcome migliore in termini di PFS nella coorte di pazienti primari (p=0.0340). Lo sviluppo di complicanze post-operatorie in pazienti con cordoma primario rappresentava un importante fattore prognostico correlato sia ad OS che a PFS (p≤0.0001 e 0.0360, rispettivamente). Nella coorte di cordomi recidivi, ∆KPS correlava sia a OS che a PFS (p=0.0010 e 0.0180, rispettivamente). Inoltre, il trattamento radioterapico postoperatorio correlava ad un aumento di OS e PFS (p=0.0020 e p=0.0100, rispettivamente). I seguenti fattori si sono rivelati predittori statisticamente significativi sia di PFS che di OS nel modello di regressione logistica: il grado di impregnazione contrastografica alla RM (intenso o lieve/nessuno), la presenza di deficit motori preoperatori (si o no) e lo sviluppo di complicanze post-operatorie (si o no). Una scala è stata sviluppata con score compresi tra 0 e 17 (Nagelkerke’s pseudo R2=0.656). Le specie totali di ceramidi e diidroceramidi nei cordomi primari erano 808.4±451.4 pmol/mg di proteine (522.5-1760.2) e 30.7±16.4 pmol/mg (17.6-62.4), rispettivamente. Le specie totali di ceramidi e diidroceramidi nei cordomi recidivi erano 1488.1±763.8 pmol/mg (540.7-2787.5) e 67.2±45.5 pmol/mg (9.0-145.6), rispettivamente. Le specie totali di ceramidi erano significativamente più elevate nei cordomi recidivi sottoposti a precedente resezione chirurgica e radioterapia rispetto ai cordomi primari (p=0.0496). Le specie totali di ceramidi e diidroceramidi nel gruppo "intensa impregnazione contrastografica" erano 1597.6±737.8 pmol/mg (592.7-2787.5) e 69.1±45.0 pmol/mg (17.8-145.6), rispettivamente. Le specie totali di ceramidi e diidroceramidi nel gruppo "nessuna o lieve impregnazione contrastografica" erano 664.7±120.4 pmol/mg (522.5-826.0) e 31.5±13.6 pmol/mg (17.6-53.6), rispettivamente. Ceramidi e diidroceramidi totali erano significativamente più alti nei cordomi ad “intensa impregnazione contrastografica” rispetto ai cordomi "nessun o lieve impregnazione contrastografica" (p=0.0290 e p=0.0186, rispettivamente). Analizzando l'associazione tra livelli di ceramidi e MIB-1 all'interno di ciascun paziente con cordoma della base cranica, i livelli di ceramidi totali hanno mostrato un'associazione forte (r=0.7257, r2=0.5267) con la colorazione MIB-1 (p=0.0033). Analizzando l'associazione tra i livelli di diidroceramidi e MIB-1 all'interno di ciascun paziente con cordoma della base cranica, i livelli totali di diidroceramidi hanno mostrato anche un'associazione forte (r=0.6733, r2=0.4533) con MIB-1 (p=0.0083). Tra le singole specie di ceramidi, Cer C24: 1 (r=0.8814, r2=0.7769, p≤0.0001), DHCer C24: 1 (r=0.8429, r2=0.7104, p=0.0002) e DHCer C18:0 (r=0.9426, r2=0.8885, p≤0.0001) hanno mostrato una correlazione significativa con il MIB-1. Conclusioni. L’analisi clinica ha dimostrato che la sintomatologia preoperatoria (deficit motori e a carico dei nervi cranici), la posizione anatomica (forame giugulare, dislocazione del tronco encefalico), le caratteristiche chirurgiche (estensione della resezione tumorale ed esperienza del chirurgo operatore), la presenza di complicanze postoperatorie e il declino del KPS si sono rivelati fattori prognostici significativi. Inoltre, il grado d’impregnazione contrastografica alla RM è stato significativamente correlato sia a OS che a PFS. È stata sviluppata in via preliminare la Peri-Operative Chordoma Scale (POCS) per aiutare il clinico nella gestione personalizzata del paziente che si sottoporrà a potenziali terapie adiuvanti. L’analisi di sfingolipidi, invece, ha evidenziato come i ceramidi possano rappresentare un promettente bio-marcatore nei cordomi. In particolare, i ceramidi a catena lunga e molto lunga, come Cer C24:1 e DHCer C18:0, possono concorrere ad una prolungata sopravvivenza del tumore, aggressività e l’effettiva comprensione del loro ruolo biologico potrà far luce sui possibili meccanismi di radio-resistenza, tendenza a recidivare del cordoma e allo sviluppo di agenti che possano avere come target il metabolismo dei ceramidi. Tali risultati dovrebbero essere validati in futuri studi clinici, in vitro e in vivo più ampi per confermare questo intricato legame tra il comportamento aggressivo del cordoma e dei ceramidi.
Introduction. Skull base chordomas are rare slow-growing neoplasms that arise from notochord. Their morbidity is mainly related to highly aggressive local invasion and resistance to treatments. Due to its heterogeneous appearance and not fully understood clinical and molecular behaviors, the main goal of the present work is to identify clinical and bio-molecular markers as specific prognostic factors that could be used for the management of skull base chordoma patients. Achieving a detailed prognostic signature of skull base chordomas is of paramount importance to personalize the treatment to each specific patient. Moreover, sphingolipids analysis is emerging as a new approach in many cancers and it has never been applied in chordomas. Our aim is to investigate chordoma biological behavior and the role of ceramides production in this context of proliferation and invasion. Patients and Methods. A retrospective review of all the patients diagnosed and treated for a skull base chordoma at the Fondazione IRCCS Istituto Neurologico “Carlo Besta” between January 1992 and December 2017 has been performed. Clinical, radiological, surgical and pathological data have been collected. A prospective collection of frozen surgical specimens has been performed to analyze ceramides species in chordomas. Sphingolipids were extracted from frozen tissues and total ceramides and dihydroceramides were evaluated by liquid chromatography and mass spectrometry. Survival analysis was performed according to Kaplan-Meier method. Univariate comparisons were conducted using Mann-Whitney, Chi-square and exact Fisher test. Simple linear regression and correlation with computation of Pearson coefficients analyses were conducted. Using a logistic regression model, statistically significant predictors were rated based on their odds ratios in order to build a personalized grading scale – the Peri-Operative Chordoma Scale (POCS). Results. Eighty-seven consecutive patients were surgically treated for a skull base chordoma during the period of recruitment. Seventy-eight patients were eligible for the retrospective review. There were 38 males (48.7%) and 40 females (51.3%). The mean follow-up was 69 months (range, 3–233). One-hundred-fourteen surgical operations were performed in the initial recruitment or recurrent setting. The presence of motor deficits in skull base chordoma revealed to be a significant prognostic factor correlating with a worse PFS (p=0.0480). Calcification on KM analysis showed a correlation with better outcomes (OS) compared with tumor lacking any calcification on CT scan (p value=0.0402). The degree of MR contrast enhancement revealed to be a significant and strong prognostic factor in terms of OS and PFS (p≤0.0001 and 0.0010, respectively). Jugular foramen involvement represented a significant prognostic factor with a worse PFS in the cohort of primary skull base chordomas (p=0.0130). The presence of chordoma in the pre-brainstem cistern revealed to be a significant prognostic factor with a worse PFS in the cohort of recurrent skull base chordomas (p=0.0210). Brainstem dislocation represented a significant prognostic factor correlating with a both worse outcome in terms of OS and PFS in the cohort of recurrent skull base chordomas (p=0.0060 and 0.0030). Extent of resection represents a strong prognostic factor according to PFS in the cohort of primary skull base chordomas (p=0.0200). Patients operated by an experienced chordoma surgeon did better in terms of prolonged PFS in the cohort of primary patients (p=0.0340). Development of post-operative complications in primary skull base chordoma patients represented an important prognostic factor related to both OS and PFS (p≤0.0001 and 0.0360, respectively). In the cohort of recurrent chordomas, ∆KPS correlated to both OS and PFS (p=0.0010 and 0.0180, respectively). Moreover, post-operative radiation treatment correlated with prolonged OS (p=0.0020) and PFS (p=0.0100). The following factors were found to be statistically significant predictors of both PFS and OS in the logistic regression model: MR contrast enhancement (intense vs mild/no), preoperative motor deficit (yes vs no) and the development of any post-operative complications (yes vs no). A grading scale was obtained with scores ranging between 0 and 17 (Nagelkerke’s pseudo R2=0.656). The mean total ceramides and dihydroceramides species in primary chordomas were 808.4±451.4 pmol/mg (522.5-1760.2) and 30.7±16.4 pmol/mg (17.6-62.4), respectively. The mean total ceramides and dihydroceramides species in recurrent chordomas were 1488.1±763.8 pmol/mg (540.7-2787.5) and 67.2±45.5 pmol/mg (9.0-145.6), respectively. Total ceramides species were significantly higher in recurrent chordomas that underwent previous surgical resection and radiation therapy in comparison to the primary chordomas (p=0.0496). The mean total ceramides and dihydroceramides species in “intense enhancement” group were 1597.6±737.8 pmol/mg (592.7-2787.5) and 69.1±45.0 pmol/mg (17.8-145.6), respectively. The mean total ceramides and dihydroceramides species in “no or mild enhancement” group were 664.7±120.4 pmol/mg (522.5-826.0) and 31.5±13.6 pmol/mg (17.6-53.6), respectively. Total ceramides and dihydroceramides were significantly higher in “intense enhancement” chordomas in comparison to the “no/mild enhancement” chordomas (p=0.0290 and p=0.0186, respectively). Analyzing the association between ceramides level and MIB-1 within each skull base chordoma patient, total ceramides level showed a strong association (r=0.7257, r2=0.5267) with MIB-1 staining (p=0.0033). Analyzing the association between DHCer level and MIB-1 within each skull base chordoma patient, total DHCer level showed also strong association (r=0.6733, r2= 0.4533) with MIB-1 staining (p= 0.0083). Among the single ceramides species Cer C24:1 (r=0.8814, r2=0.7769, p≤0.0001), DHCer C24:1 (r=0.8429, r2=0.7104, p=0.0002) and DHCer C18:0 (r=0.9426, r2=0.8885, p≤0.0001) levels showed a significant correlation with MIB-1 staining. Final candidate predictive factors that well fitted the regression model were: cer24:1 (r=0.824, p≤0.001), and DHCer C18:0 (r=0.748, p=0.002). Conclusion. Our clinical analysis showed that pre-operative clinical symptoms (motor and cranial nerve deficits), anatomical location (jugular foramen, pre-brainstem cisterns and brainstem dislocation), surgical features (extent of tumor resection and surgeon’s experience), development of post-operative complications and KPS decline represent significant prognostic factors. The degree of MR contrast enhancement significantly correlated to both OS and PFS. We also preliminarily developed the Peri-Operative Chordoma Scale (POCS) to aid the practitioner in the personalized management of patients undergoing potential adjuvant therapies. Our lipid analysis showed ceramides as promising tumoral bio-markers in skull base chordomas. Long and very long chain ceramides, such as Cer C24:1 and DHCer C24:1, may be related to a prolonged tumor survival, aggressiveness and the understanding of their effective biological role will hopefully shed lights on the mechanisms of chordoma radio-resistance, tendency to recur and use of agents targeting ceramide metabolism. Such results should be validated in future larger clinical, in-vitro and in-vivo studies to confirm such intricate link between ceramides and chordoma aggressive behavior.

The use of stem cells is a promising therapeutic approach for tissue engineering by their ability to boost tissue regeneration, and to model in vitro human genetics disorders since it provides continuous supplies of cells with differentiation potential. Our study has been focused in the identification of molecules or mechanisms that could contribute to a better osteogenesis in mesenchymal stem cells (MSC). To achieve our goals we have explored the osteopontential differences of stem cells from different sources. In this regard, we have observed that MSCs from human exfoliated deciduous teeth (SHED) presented higher in vitro osteogenic differentiation potential (OD) as compared to MSCs derived from human adipose tissue (hASCs). Through microarray analysis and cell sorting, we have shown that IGF2 and CD105 expression levels contribute to these osteopontential cell differences, that is, higher IGF2 expression levels and lower CD105 expression levels were associated with the increased osteogenic potential of SHED as compared to hASCs. The molecular mechanisms associated with the diferent expression levels of IGF2 and CD105 in these cells were also investigated. Despite the advantages of adult MSCs they can exhibit drawbacks such as restricted self-renewal and limited cell amounts. Induced Pluripotent Stem Cells (iPSC) technology has emerged as an alternative cell source, as they provide more homogeneous cellular populations with prolonged self-renewal and higher plasticity. We verified that the OD of MSC-like iPSC differs from MSCs and it depends on the iPSCs originating cellular source. Comparative in vitro osteogenesis analysis showed higher osteogenic potential in MSC-like cells derived from iPS-SHED when compared with MSC-like cells from iPS-FIB and SHED. iPSCs can be also used as a tool to model genetic disorders. We have thus proposed to verify if it could be possible to in vitro model Treacher-Collins syndrome, a condition with deficient craniofacial bone development. We have compared the effects of pathogenic mutations in TCOF1 gene in cell proliferation, differentiation potential between MSCs, dermal fibroblasts, neural-crest like and MSC-like cells differentiated from iPSCs.TCS cells showed changes in cell properties anddysregulated expression of chondrogenesis markers during osteogenic and chondrogenic differentiation. In summary, the comparative analysis of stem cells of different sources allow us to identify markers that may facilitate osteogenesis and that it is possible to establish an in vitro model to Treacher-Collins syndrome
O uso de células-tronco trata-se de uma abordagem terapêutica promissora para a engenharia de tecidos, devido à sua capacidade na regeneração de tecidos, e para modelamento in vitro de distúrbios genéticos humanos, uma vez que fornece um abastecimento contínuo de células com potencial de diferenciação. Nosso estudo se propos a identificar moléculas e mecanismos que contribuem na otimização da osteogênese de células-tronco mesenquimais (MSCs). Para atingir nossos objetivos exploramos as diferenças no potencial osteogênico (PO) de MSCs de diferentes fontes. Observamos que MSCs de polpa de dente decíduo humano (SHED) apresentaram maior PO em comparação com as MSC derivadas de tecido adiposo humano (hASCs). Através de análise de microarray de expressão e cell sorting, demonstramos que os níveis de expressão de IGF2 e CD105 contribuem para as diferenças do PO, onde a maior expressão de IGF2 e menor expressão de CD105 estão associadas a maior PO em SHED quando comparado as hASCs. Também investigamos os mecanismos moleculares associados aos diferentes níveis de expressão de IGF2 E CD105 em ambas as fontes celulares. Apesar das vantagens, as MSCs podem apresentar pontos negativos como restrita auto-renovação e menor quantidade de células. Células-tronco pluripotentes induzidas (iPSC) surgem como uma fonte celular alternativa, proporcionando populações celulares homogêneas com auto-renovação prolongada e maior plasticidade. O PO de MSC-like iPSC difere de MSCs, e este potencial é dependente da fonte celular em que as iPSCs são obtidas. Análise comparativa de PO in vitro demonstrou maior osteogênse em células MSC-like derivadas de iPS-SHED quando comparada as células MSC-like de iPSCs-fibroblastos e SHED. iPSCs também podem ser utilizadas como ferramenta para investigar doenças genéticas humanas. Propomos a modelagem in vitro da síndrome de Treacher-Collins (TSC), doença que acomete as estruturas craniofaciais durante o desenvolvimento ósseo. Comparamos os efeitos de mutações patogênicas no gene TCOF1 na proliferação celular, potencial de diferenciação entre MSCs, fibroblastos dérmicos, neural-crest like e células MSC-like diferenciadas de iPSCs. Células de pacientes TCS exibiram alterações em propriedades celulares e na expressão de marcadores osteogênicos e condrogênicos. Em resumo, a análise comparativa de células-tronco de diferentes fontes permitiu a identificação de marcadores e mecanismos que podem facilitar a osteogênese e tambem demonstramos que é possível modelar in vitro a síndrome de Treacher-Collins

Barley (Hordeum vulgare L.) is one of the most important cereal crops in North Dakota, which ranks second amongst all states for barley production in the United States. Barley is used for the production of malt, which is used for brewing beer. The malting and brewing industries set strict standards for malt quality; yet, determining malt quality of experimental barley lines is very expensive. For this reason, quality is typically determined at the latter stages of the breeding program, resulting in rejection of many genotypes after large investments for agronomic performance, disease resistance, and end-use quality evaluations have occurred. High quality malt cultivars must possess numerous genetically controlled characteristics. This limits the effectiveness of phenotypic selection for malt quality. The use of marker-assisted selection (MAS) may enable breeders to eliminate lines with undesirable traits earlier in the breeding process, reducing costs, and improving genetic gain. In spite of the large number of mapped QTLs, few examples exist in the literature in which QTL analysis and MAS have been applied to the genetic improvement of malting barley. This research was initiated to identify robust marker-trait associations for malting quality, disease resistance, and agronomic traits utilizing genome-wide association mapping of selected NDSU two-rowed lines. Our research successfully identified numerous marker-trait associations for the traits evaluated to be used for MAS to improve the North Dakota State University barley breeding program.
American Malting Barley Association

The clinical course of chronic lymphocytic leukemia (CLL) is highly heterogeneous, which has prompted the search for biomarkers that can predict prognosis in this disease. The IGHV gene mutation status and certain genomic aberrations have been identified as reliable prognostic markers of clinical outcome for this disorder. However, the search for more feasible prognostic markers in CLL is still being pursued. Recently, certain single nucleotide polymorphisms (SNPs) in the GNAS1, BCL2 and MDM2 genes and the RNA expression levels of the LPL, ZAP70, TCL1, CLLU1 and MCL1 genes were suggested as novel prognostic markers in CLL. In papers I-III, we performed genotyping analyses of the GNAS1 T393C, BCL2 -938C>A and MDM2 SNP309 polymorphisms in 268-418 CLL patients and related the genotypes with clinical data. Association studies between the polymorphisms and established prognostic markers (i.e. IGHV mutation status, genomic aberrations, CD38 expression) were also performed. Our studies did not find any significant relationship between these SNPs with either clinical outcome or other known prognostic markers in CLL. In paper IV, we measured the RNA expression levels of LPL, ZAP70, TCL1, CLLU1 and MCL1 in 252 CLL cases and correlated these levels with clinical outcome. Here, we verified that high expression of all these RNA-based markers, except MCL1, were associated with an unfavourable prognosis. We also confirmed a close relationship between IGHV mutation status and the RNA-based markers, especially for LPL and CLLU1 expression. Among the RNA-based markers, multivariate analysis revealed LPL expression as the strongest independent prognostic marker for overall survival and time to treatment. Furthermore, the RNA-based markers could add further prognostic information to established markers in subgroups of patients, with LPL expression status giving the most significant results. In summary, data from papers I-III could not verify the GNAS1 T393C, BCL2 -938C>A and MDM2 SNP309 polymorphisms as prognostic markers in CLL. Future SNP markers must hence be confirmed in large, independent cohorts before being proposed as prognostic marker in CLL. In paper IV, we conclude that LPL expression appears to be the strongest among the RNA-based markers for CLL prognostication. Further efforts to standardize LPL quantification are required before it can be applied in the clinical laboratory to predict clinical outcome in this disease.

Abstract Ovarian cancer is the leading cause of death from gynaecological cancers in the Western world. Ovarian cancer comprises of tumours with distinct behaviour and individually different responses to chemotherapy, even within the same histology. Unfortunately, there are no molecular markers in clinical use to either distinguish between patients with better and worse prognosis or to predict individual chemosensitivity. The comprehension of the molecular effects of chemotherapeutic drugs is a prerequisite for finding predictive molecular factors for chemoresponse and prognosis. Some proteins in molecular pathways contributing to DNA damage response, angiogenesis and oxidative stress have been implicated in ovarian cancer prognosis. In this study, the responses in p53 pathway and among angiogenesis-related factors to chemotherapeutic drugs were analysed in ovarian cancer cell lines. In OVCAR-3 cells with mutated p53, cisplatin but not docetaxel induced p14ARF, an important regulator of p53, at mRNA and protein level. Cisplatin also significantly increased the mRNA expression of angiogenesis-related factors TSP-1, BMP-4, ET-1 and PlGF-2 while an equivalent dose of docetaxel had only minor effects. In clinical ovarian carcinomas, the expression of BMP-4, TSP-1 and CD105 as well as the marker of oxidative stress derived DNA damage, 8-OHdG, and peroxiredoxin antioxidants were analysed by immunohistochemistry. High expression of BMP-4 and cytoplasmic peroxiredoxin IV were associated with better prognosis, while high 8-OHdG expression associated with shorter survival. Explant cultures of fresh ovarian tumour tissue were used for the evaluation of individual responses of p53 and Hdm2 after in vitro treatments of the explant cultures by carboplatin or docetaxel. Major differences between the individual tumours were found, especially in the responses of p53 to carboplatin. The results of this study suggest, that BMP-4, 8-OHdG and peroxiredoxin IV may serve as prognostic markers in ovarian cancer. The differences shown in the molecular responses to platinum and taxane drugs may have value in tailoring individual chemotherapy. Also, fresh ovarian cancer tissue explant culture is worth further studies as a predictive method for analysing individual tumour responses for chemotherapeutic agents
Tiivistelmä Munasarjasyöpä on suurinta kuolleisuutta aiheuttava gynekologinen syöpä läntisessä maailmassa. Munasarjakasvaimet eroavat toisistaan niin käyttäytymiseltään kuin yksilölliseltä sytostaattihoitovasteeltaan, jopa sama histologisen tyypin sisällä. Kliinisessä käytössä ei valitettavasti ole sellaisia molekulaarisia merkkiaineita, jotka erottaisivat toisistaan paremman ja huonomman ennusteen kasvaimet tai ennustaisivat yksilöllistä solunsalpaajaherkkyyttä. Hoitovastetta ja potilaan prognoosia ennustavien merkkiaineiden löytämisen edellytys on kemoterapian molekyylitason vaikutusten ymmärtäminen. DNA vaurion tunnistamiseen, angiogeneesiin ja oksidatiiviseen stressiin liittyvien vaikutusreittien joillakin proteiineilla on ehdotettu olevan ennusteellista merkitystä munasarjasyövässä. Tässä väitöskirjatyössä analysoitiin munasarjasyöpäsoluja käyttäen p53 vaikutusreitin ja eräiden angiogeneesiin liittyvien tekijöiden vasteita sytostaateille. Mutatoitunutta p53 proteiinia kantavissa OVCAR-3 soluissa sisplatiini, toisin kuin dosetakseli, indusoi p53 proteiinin tärkeää säätelijää, p14ARF:a sekä mRNA- että proteiinitasolla. Sisplatiini lisäsi merkittävästi myös usean angiogeneesiin liittyvän tekijän (TSP-1, BMP-4, ET-1 ja PlGF-2) mRNA:ta. Dosetakselin vaikutukset vastaavalla annoksella olivat vähäiset. Kliinisissä munasarjasyövissä BMP-4, TSP-1 ja CD105 sekä oksidatiivisen stressin aiheuttaman DNA-vaurion merkkiaineen, 8-OHdG:n sekä peroksiredoksiiniantioksidanttien ilmeneminen analysoitiin immunohistokemiallisesti. BMP-4:n ja sytoplasmisen peroksiredoksiini IV:n vahva ilmentyminen liittyivät parempaan ennusteeseen, kun taas 8-OHdG:n vahva ilmentyminen liittyi huonompaan elinajan ennusteeseen. Tuoreen munasarjasyöpäkudoksen eksplanttiviljelyn avulla selvitettiin p53 ja Hdm2 proteiinien vasteita syöpäkudoksen karboplatiini- tai dosetakseli-käsittelyille. Selkeitä yksilökohtaisia eroja havaittiin erityisesti karboplatiinin aiheuttamissa p53 vasteissa niin eri potilaiden kuin eri histologisten kasvaintyyppien välillä. Tämän väitöskirjatutkimuksen tulokset antavat viitteitä BMP-4:n, 8-OHdG:n ja peroksiredoksiinin mahdollisesta ennusteellisesta merkityksestä munasarjasyövässä. Erot platinayhdisteiden ja taksaanien välillä saattavat osoittautua merkittäviksi yksilöllisiä syövän hoitoja räätälöitäessä. Tuoreen munasarjasyöpäkudoksen eksplanttiviljelyn mahdollisuuksia yksilöllisten kasvainten hoitovasteiden ennustamisessa kannattaa selvittää jatkotutkimuksin

Prostate cancer is a significant health problem worldwide. Glucocorticoids, including' dexamethasone have formed the backbone of treatment of androgenindependent disease for the past 50 years and are given with docetaxel in the only therapy with a proven survival benefit in this setting. This study explored the mecha'nism of dexamethasone action in the treatment of androgen-independent prostate cancer (AIPC). In the in vitro study' dexamethasone administration induced a suppression of NFKB transcriptional activity in AIPC cells, resulting in a decreased transcription . arid/or secretion of the pro-angiogenic factors interleukin-8 and VEGF. In addition, co-administration of dexamethasone attenuated the docetaxel-induced .- '..: .. AP-1 and NF-KB transcriptional activity and abrogated the IL-8 gene transcription . - - -- - ·L and secretion in these cells and endothelial cells. In a novel finding, addition of dexamethasone potentiated the pronounced anti-angiogenic activity of docetaxel as assessed by an in vitro angiogenesis assay. Since no modulation of docetaxel cytotoxicity in endothelial cells by addition of. dexamethasone was observed, these results suggest that dexamethasone contributes to the efficacy of docetaxel through reduction of the docetaxel-induced increase of pro-angiogenic factors both in prostate cancer and endothelial cells, which translates into inhibition of angiogenesis. In the clinical study, the PSA response rate was 63%. Serum IL-8 was elevated in all 11 oatients for whom data is available. However. at this interim analvsis Supplied by The British Library - 'The world's knowledge' I I, I ' serum IL-8 levels were not consistently modified following dexamethasone therapy. However, when IL-8 is analysed as a binary variable, low IL-8 is associated with a prolonged time to biochemical progression which does not reach statistical significance at this time. Similarly, CRP levels were not affected consistently by dexamethasone but baseline CRP was lower in patients who achieved a PSA response than in those who did not respond, though this difference was not statistically significant.

The Crimson-spotted rainbowfish (Melanotaenia fluviatilis) from the Murray-Darling basin of Australia is a common indicator species in Australian ecotoxicology. Biochemical changes have been investigated in this species, but not molecular markers of ecotoxicological interest. In this study genes of M. fluviatilis were isolated using a cDNA library and sequences analysed. Of 345 randomly selected clones, 94 shared similarity with 26 different genes in other organisms in public databases. Amongst these, reproductive genes coding for vitellogenin, retinol binding protein, sialyltransferase and zona pellucida protein were considered of interest in ecotoxicology. The vitellogenin gene was selected for study as it has been widely used as a molecular marker of exposure to 17â-estradiol (E2) in teleosts. Gene expression was examined via northern blot, RT-PCR and Real-Time PCR relative to the housekeeping gene (18S rRNA). The expression of vitellogenin mRNA was observed a t 12 hours post-exposure, peaked at 48 hours according to northern blot analysis; and cleared within 4 days, partly consistent with RT-PCR. However, Real-time PCR yielded an inconclusive result, probably due to differences between pooled and individual samples. Vitellogenin in blood plasma was confirmed by western blot, found to be significantly increased and retained in the plasma in fish treated with E2 compared to controls. It was concluded that vitellogenin mRNA is a molecular marker of exposure to 17â-estradiol in the rainbowfish, and could potentially be used as a marker of exposure to environmental estrogenic chemicals. Further investigations of the expression of genes in the cDNA library, could establish other molecular markers of ecotoxicological interest in M. fluviatilis.