Hereditary risk factors for stroke in humans - Association studies with emphasis on familial and genotypic factors

Background Stroke is a serious vascular disorder that comprises intracerebral hemorrhages, subarachnoid hemorrhages and ischemic stroke (IS). The etiology of stroke, including hereditary components induced by cellular mechanisms, is therefore a research field of vital importance. The aim of this thesis was to assess possible genetic impact on stroke risk. We thus evaluated family history of stroke-related individual traits as well as allelic variations in selected candidate genes. Methods Association studies, primarily of Lund Stroke Register data, were fundamentals in the analyses in order to find possible genetic association with stroke risk. Hereditary risk factors, based on family-history data and candidate gene studies, were considered. Statistical methods for assessing the data, including basic chi-square tests of two-by-two tables as well as various logistic regression approaches and meta-analysis applications using the DerSimonian-Laird method, were used. TOAST subtypes of ischemic stroke were considered when available. Also, 25 coronary artery disease (CAD) susceptible SNPs from various genetic loci were joined together in risk scores and tested against IS risk by logistic regression. Results Paper I: The prevalence of stroke or TIA among first-degree relatives may affect the proband’s stroke risk (odds ratio, OR=1.74; 95% confidence interval, CI: 1.36-2.22), especially when considering mothers and offsprings (OR=2.04; 95% CI: 1.30-3.20). No such association was seen at all between spouses. Papers II-III: SNP rs12188950 was significantly associated with IS in Paper II (OR=0.72; 95% CI: 0.58-0.91; N=1324), but not in Paper III (OR=0.93; 95% CI: 0.83-1.05; N=4692) where a different sample representing an analogous Swedish population was used. Paper IV: SNP rs4977574 on chromosome 9p21 was related to IS risk (OR=1.12; 95% CI: 1.04-1.20) and large vessel disease risk (OR=1.36; 95% CI: 1.13-1.64). This genetic effect of chromosome 9p21 on IS was however already known. None of the other 24 SNPs or compiled risk scores were significant. Conclusions and discussion Significant transmission of stroke from parents to offsprings but not between spouses suggests a genetic inheritance component. But, for SNPs representing some particular carefully selected genes, the findings regarding possible impact on IS were not that clear: Ambiguous results were obtained, many significance tests were also negative. Moreover, we could not generally find significant associations between SNPs susceptible for CAD and IS risk

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open problem in structural biology, pursued with increasing vigor as more and more protein sequences continue to fill the data banks. Within this task lies a statistical inference problem, rooted in the following: correlation between two sites in a protein sequence can arise from firsthand interaction but can also be network-propagated via intermediate sites; observed correlation is not enough to guarantee proximity. To separate direct from indirect interactions is an instance of the general problem of inverse statistical mechanics, where the task is to learn model parameters (fields, couplings) from observables (magnetizations, correlations, samples) in large systems. In the context of protein sequences, the approach has been referred to as direct-coupling analysis. Here we show that the pseudolikelihood method, applied to 21-state Potts models describing the statistical properties of families of evolutionarily related proteins, significantly outperforms existing approaches to the direct-coupling analysis, the latter being based on standard mean-field techniques. This improved performance also relies on a modified score for the coupling strength. The results are verified using known crystal structures of specific sequence instances of various protein families. Code implementing the new method can be found at http://plmdca.csc.kth.se/.Comment: 19 pages, 16 figures, published versio

Insättningsgaranti - en komparativ studie av de svenska och norska insättningsskyddssystemen

Insättningsskydd är vanligt förekommande i de flesta industrialiserade länder idag. Den främsta anledningen till att insättningsskydd införts är för att skydda konsumenter från förluster vid bankfallissemang, och det är detta som är systemens grundläggande funktion. Insättningsskyddet kan emellertid också ses som en komplettering av de mer övergripande reglerna för banklicensiering (oktroj) och tillsyn. Det gemensamma målet för det här regelpaketet är att försöka skydda insättare från förluster. Insättningsskydd medför, förutom konsumentskydd, även ett systemskydd. Systemskyddet kommer av att insättare oftast känner ett större förtroende för banksystemet ifall deras insättningar är säkra, och detta kan hindra så kallade bank runs (uttagsanstormningar). Den största nackdelen med insättningsskydd är risken för moral hazard-problem. Om alla insättningar är försäkrade genom ett insättningsgaranti-system, kan både banken och insättaren öka sitt risktagande till en vårdslös nivå. Ytterligare ett problem med insättningsgaranti är hur finansieringen av systemet ska ske. Genom EG-direktiv 94/19/EG om system för garanti av insättningar blev EU:s medlemsstater förpliktigade att införa insättningsgarantisystem. Direktivet är ett minimidirektiv som fastställer vissa grundläggande delar i ett insättningsgarantisystem som medlemmarna måste införa. Sverige inträdde som medlem i EU 1995 och implementerade direktivet genom lag (1995:1571) om insättningsgaranti som trädde ikraft den 1 januari 1996. EG-direktivet infogades i EES-avtalet under 1994, och därför tvingades även Norge uppfylla direktivets bestämmelser. Detta gjordes genom införandet av lov om sikringsordninger for banker, forsikringsselskapenes garantiordninger og offentlig administrasjon m.v. av finansinstitusjoner som trädde ikraft den 1 januari 1997. Trots en gemensam grund i EG-direktivet finns det stora skillnader mellan de svenska och norska insättningsgarantisystemen. Den norska insättningsgarantin täcker mycket högre insättningsbelopp och omfattar fler typer av insättningar. Det norska systemet kan också ingripa på ett mycket tidigare stadium, och hjälpa banker att undvika konkurser. De båda systemen har sina för- och nackdelar, men i internationella sammanhang har Norges insättningsgaranti fått ta emot mest kritik. Det är framför allt Norges höga ersättningsnivåer som har kritiserats, och denna kritik har framförts av bl.a. IMF

Nanog, Oct4 and Tet1 interplay in establishing pluripotency

A few central transcription factors inside mouse embryonic stem (ES) cells and induced pluripotent stem (iPS) cells are believed to control the cells’ pluripotency. Characterizations of pluripotent state were put forward on both transcription factor and epigenetic levels. Whereas core players have been identified, it is desirable to map out gene regulatory networks which govern the reprogramming of somatic cells as well as the early developmental decisions. Here we propose a multiple level model where the regulatory network of Oct4, Nanog and Tet1 includes positive feedback loops involving DNA-demethylation around the promoters of Oct4 and Tet1. We put forward a mechanistic understanding of the regulatory dynamics which account for i) Oct4 overexpression is sufficient to induce pluripotency in somatic cell types expressing the other Yamanaka reprogramming factors endogenously; ii) Tet1 can replace Oct4 in reprogramming cocktail; iii) Nanog is not necessary for reprogramming however its over-expression leads to enhanced self-renewal; iv) DNA methylation is the key to the regulation of pluripotency genes; v) Lif withdrawal leads to loss of pluripotency. Overall, our paper proposes a novel framework combining transcription regulation with DNA methylation modifications which, takes into account the multi-layer nature of regulatory mechanisms governing pluripotency acquisition through reprogramming

En undersökning av lipidhalt och lipidsammansättning i Atlantlax, pinklax och pangasiusmal, från lokala livsmedelsbutiker i Uppsala

The aim of this study is to investigate the lipid content and lipid composition of fatty acids in Atlantic salmon (Salmo salar), pink salmon (Oncorhynchus gorbuscha) and striped catfish (Pangasius hypophthalmus), obtained at the local retailers in Uppsala, Sweden. Then explore the cause of the differences in the fatty acids between the three fish species. In addition, the present data will be compared to the data available at National Food Ad-ministration in Sweden (SLV) and National Institute of Nutrition and Seafood Research in Norway (NIFES). Fish is a main food that provides n-3 long chain polyunsaturated fatty acids (LCPUFA), and is to many people known to be a healthy choice as food. It is particularly the n-3 LCPUFAs that have been shown to have positive effects on for example cardiovascular disease and cancer. Docosahexaenoic (DHA) and eicosapentaenoic (EPA) are n-3 LCPUFAs, present in fish and fish oils. The demand for fish raw material as fish feed is rising around the world, and this depends on a steady increase of aquaculture production. A change from using fish raw material to use more ingredients based on vegetables have been investigated. There is a consequence of this change from fish raw material to plant based material on human health, where the degree of long chain n-3 fatty acids have been lowered in the fish and the beneficial health effects of fish on humans is therefore decreas-ing. In vegetable oils there is a high concentration of n-6 and n-9 fatty acids that is mostly linoleic acid and oleic acid respectively. In vegetable oils there are also low or moderate levels of n-3 fatty acids (excluding linseed oil) of mostly α-linolenic acid. Although vege-table oils do not have the long chain highly unsaturated fatty acids (LCHUFA), EPA and DHA. In this study seven different samples were taken from Atlantic salmon, pink salmon and striped catfish. The samples all have different origin and label, and all the samples were from a farmed fish fillet except one wild fish. The samples tested in this study were all homogenized and the fat of the samples was extracted. Fatty acid composition was ana-lyzed by a gas chromatograph (GC). The fat content in the four farmed Atlantic salmon samples was: 7.0, 7.6, 9.4 and 7.4 % respectively. The fat content in the wild pink salmon was: 3.0 %. The fat content in the two farmed striped catfish samples was 0.3 and 0.5 %. The proportion of fatty acids was all measured in % of total fatty acids. The percentage of EPA (20:5 n-3) and DHA (22:6 n-3) was higher in the farmed Atlantic salmon and wild pink salmon, compared to the farmed striped catfish, as expected. Linoleic acid (18:2 n-6) was significantly higher in the farmed striped catfish, and lower in both the farmed Atlantic salmon and wild pink salmon. α-linolenic acid (18:3 n-3) was present at a smaller percentage in the farmed striped catfish than in both the farmed Atlantic salmon and wild pink salmon. The n3/n6 ratio was signifi-cantly higher in the wild pink salmon, than in both the farmed Atlantic salmon and farmed striped catfish

Variations in apolipoprotein D and sigma non-opioid intracellular receptor 1 genes with relation to risk, severity and outcome of ischemic stroke

Background: In experimental studies, the apolipoprotein D (APOD) and the sigma receptor type 1 (SIGMAR1) have been related to processes of brain damage, repair and plasticity. Methods: We examined blood samples from 3081 ischemic stroke (IS) patients and 1595 control subjects regarding 10 single nucleotide polymorphisms (SNPs) in the APOD (chromosomal location 3q29) and SIGMAR1 (chromosomal location 9p13) genes to find possible associations with IS risk, IS severity (NIHSS-score) and recovery after IS (modified Rankin Scale, mRS, at 90 days). Simple/multiple logistic regression and Spearman's rho were utilized for the analyses. Results: Among the SNPs analyzed, rs7659 within the APOD gene showed a possible association with stroke risk (OR = 1.12; 95% CI: 1.01-1.25; P = 0.029) and stroke severity (NIHSS >= 16) (OR = 0.70; 95% CI: 0.54-0.92; P = 0.009) when controlling for age, sex and vascular risk factors for stroke. No SNP showed an association with stroke recovery (mRS). Conclusions: We conclude that the SNP rs7659 within the APOD gene might be related to risk and severity of ischemic stroke in patients

DNA methylation in human epigenomes depends on local topology of CpG sites

In vertebrates, methylation of cytosine at CpG sequences is implicated in stable and heritable patterns of gene expression. The classical model for inheritance, in which individual CpG sites are independent, provides no explanation for the observed non-random patterns of methylation. We first investigate the exact topology of CpG clustering in the human genome associated to CpG islands. Then, by pooling genomic CpG clusters on the basis of short distances between CpGs within and long distances outside clusters, we show a strong dependence of methylation on the number and density of CpG organization. CpG clusters with fewer, or less densely spaced, CpGs are predominantly hyper-methylated, while larger clusters are predominantly hypo-methylated. Intermediate clusters, however, are either hyper- or hypo-methylated but are rarely found in intermediate methylation states. We develop a model for spatially-dependent collaboration between CpGs, where methylated CpGs recruit methylation enzymes that can act on CpGs over an extended local region, while unmethylated CpGs recruit demethylation enzymes that act more strongly on nearby CpGs. This model can reproduce the effects of CpG clustering on methylation and produces stable and heritable alternative methylation states of CpG clusters, thus providing a coherent model for methylation inheritance and methylation patterning.Cecilia Lövkvist, Ian B. Dodd, Kim Sneppen and Jan O. Haerte

A Common Missense Variant in the ATP Receptor P2X7 Is Associated with Reduced Risk of Cardiovascular Events

BACKGROUND AND PURPOSE: Extracellular adenosine triphosphate (ATP) regulates inflammatory cells by activation of the P2X(7) receptor. We hypothesized that polymorphisms in P2RX7 influence the risk of ischemic heart disease (IHD), ischemic stroke (IS) and cardiovascular risk factors and tested this hypothesis using genetic association studies. METHODS: Two loss-of-function SNPs in P2RX7 were genotyped in 1244 IHD cases and 2488 controls as well as 5969 individuals with cardiovascular risk factors. Eleven SNPs in a 250 kb region on chromosome 12 spanning P2RX7 as well as neighboring genes OASL, P2RX4 and CAMKK2 were genotyped in 4138 individuals with IS and 2528 controls. Association was examined using linear and logistic regression models with an additive genetic model. RESULTS: The common loss-of-function variant rs3751143 was significantly associated with a decreased risk of IHD in smokers (P = 0.03) as well as decreased risk of IS (OR 0.89; 95% CI = 0.81-0.97; P = 0.012). In addition, an intronic SNP in CAMKK2, rs2686342, were associated with a decreased risk of IS (OR 0.89; 95% CI = 0.82-0.97; P = 0.011). In subgroup analyses, both SNPs were associated with decreased risk of IS in individuals with hypertension (P = 0.045 and 0.015, respectively). CONCLUSIONS: A common loss-of-function missense variant in the gene encoding the P2X(7) receptor is associated with reduced risk of IS and with IHD in smokers. These findings might implicate a role of purinergic signaling in atherogenesis or atherothrombosis

Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states

Published online 27 November 2013Inheritance of 5-methyl cytosine modification of CpG (CG/CG) DNA sequences is needed to maintain early developmental decisions in vertebrates. The standard inheritance model treats CpGs as independent, with methylated CpGs maintained by efficient methylation of hemimethylated CpGs produced after DNA replication, and unmethylated CpGs maintained by an absence of de novo methylation. By stochastic simulations of CpG islands over multiple cell cycles and systematic sampling of reaction parameters, we show that the standard model is inconsistent with many experimental observations. In contrast, dynamic collaboration between CpGs can provide strong error-tolerant somatic inheritance of both hypermethylated and hypomethylated states of a cluster of CpGs, reproducing observed stable bimodal methylation patterns. Known recruitment of methylating enzymes by methylated CpGs could provide the necessary collaboration, but we predict that recruitment of demethylating enzymes by unmethylated CpGs strengthens inheritance and allows CpG islands to remain hypomethylated within a sea of hypermethylation.Jan O. Haerter, Cecilia Lövkvist, Ian B. Dodd and Kim Sneppe