40 research outputs found
Increased lipid concentrations are common in <i>STHdh</i><sup>Q111/Q111</sup> cell pellets.
<p>A) Strip-plots summarize the logarithm of the concentration ratios of metabolites altered in mutant, compared to wild-type, in cell pellets (left) or growth media (right) at a false-discovery rate of 10% and fold-change cut-off of +/- 30%. Metabolites whose concentrations are increased in mutant samples are indicated with a blue square, while those metabolites that are decreased in mutant samples are shown in a green. B) Normalized lipid peak values in replicate <i>STHdh</i><sup>+/+</sup> and <i>STHdh</i><sup>Q111/Q111</sup> cell pellets are depicted in the heat-map with higher concentrations in red and lower concentrations in blue. For comparison across lipid species, LC-MS peak heights were converted to a Z-score by subtracting the mean concentration of each species and dividing the remainder by the standard deviation. Each lipid class includes species with variable chain lengths and number of saturated bonds (columns). With the exception of lysophosphatidylcholine species, most lipid species are increased in mutant cells. C) The distribution of the actual mutant / wild type peak ratios for all measured lipid concentrations is shown in red. To test for lipid accumulation in mutant cells, the same distribution was calculated 1,000 using the same data with permuted genotype labels; those distributions are shown in gray.</p
Coherently increased lipids in striatal cells and striatal tissue from <i>Hdh</i><sup><i>Q111/+</i></sup> mice.
<p>A. The mutant/wild-type ratio of each lipid species is indicated on the heatmap (red = 0.5, yellow = 1.0 and green = 1.5). In the panel on the left, lipid species (rows, labels omitted for clarity) were sorted by their genotype p-value in the striatum. Sorting in this way reveals a clustering of green boxes near the top of the heatmap, suggesting an enrichment of accumulated lipids in the striatum. In the panel on the right, the same data was sorted by the genotype p-value in the cerebellum—no such clustering is observed. Metabolites nominally significant in a given tissue are outlined in black. The class of each lipid is indicated in the text, with neutral lipid species indicated in bold. B. The mutant/wild-type ratio of each lipid species that was quantified in both striatal tissue and striatal cells is graphed for striatal tissue (horizontal axis) and immortalized striatal cells (vertical axis); values greater than 1 indicate increased concentrations in mutant samples, while values less than 1 indicate decreased concentrations in mutant samples. The ratios in both cells and tissue for each lipid species are indicated by the position of its label. Lipids whose levels are increased in both striatal cells and tissue predominate, and are indicated by the green rectangle. Lipids with inconsistent changes between cells and tissue are in gray rectangles, while only 1 measured lipid species (C18.0.LPC) is decreased in both samples. Lipid species are indicated as CX.Y.Z, where X = total acyl chain length, Y = total number of unsaturated bonds and Z = lipid species. The lipid species graphed are D/TAG = Di-/Tri-glyceride; LPE/C = Lysophosphatidyl-ethanolamine/choline; PC = phosphatidylcholine.</p
The number of measured metabolites sensitive to <i>Htt</i> genotype, diet or to an <i>Htt</i> genotype-diet interaction varies across tissues.
<p>For each tissue, metabolite values were filtered to include only those with at least 3 non-0 values per arm of the diet/genotype study design.</p
Alterations in tissue metabolite levels in response to CAG-expansion in <i>Htt</i> and increased dietary fat.
<p>A) Summary of the number of nominally significant metabolites per tissue (as a percentage of total measured metabolites) for each tissue—heat map color indicates the number of metabolites significant at p < 0.05. B) A relatively limited number of metabolites show concordant (green text) or discordant (red text) concentration changes in response to CAG-expansion in <i>Htt</i> in the striatum and cerebellum. The striatum and cerebellum also show the largest number (4) of overlapping diet-responsive metabolites amongst tissue pairs. C) Determination of genotype using metabolite concentrations using random forests—the error rate for each tissue is shown over 500 iterations. Below, the contribution of individual metabolites to model accuracy is shown for striatum and cerebellum, the two tissues with accurate models. The y-axis indicates the increase in errors in genotype prediction (in %) after permuting the genotype labels for the indicated metabolite. D) The concentrations of lipid species important for genotype prediction in the striatum are increased in the <i>Htt</i><sup><i>Q111/Q7</i></sup> samples (PC 32:2–49% increase, p = 0.024; CE 18:0–54% increase, p = 0.004; SM 24:0–33% increase, p = 0.02; 65% increase, p = 0.06).</p
Metabolite profiles clearly discriminate tissue types.
<p>A—Linear discriminant analysis was conducted to derive linear combinations of metabolite concentrations that separate tissue types. In this approach, linear combinations of factors (here, metabolites) are constructed that maximally differentiate a factor of interest (here, tissue type). Scatter-plot matrix of the top 3 linear discriminants (linear combinations of variables) constructed reveals that they very effectively separate tissue types; the tissue type of each sample is indicated by text and color. To test the robustness of this finding, the tissue labels of each sample were randomly permuted, and the LDA analysis repeated. Increased scatter suggests that tissue-separation is much less accurate using permuted data, consistent with the hypothesis that inter-tissue variability is lower than intra-tissue variability in these samples. Linear discriminants derived from actual data are shown on the left, those derived from tissue-label permuted data are shown on the right. B—Sample concentrations of metabolites with clear tissue-specific roles; GABA is high in CNS tissues (striatum and cerebellum), and absent in peripheral tissues. The conjugated bile acid taurochenodeoxycholate are present in the liver, and to a smaller extent the plasma, but absent from other tissues.</p
Striatal enrichment of the 10 most genotype-sensitive metabolites in the striatum of <i>Htt</i><sup><i>Q111/+</i></sup> mice.
<p>Top ranked metabolites by genotype ANOVA F-statistic are included in order of magnitude. The relative integrated peak height of each metabolite in the striatum compared to the liver and cerebellum is indicated by the rank of each metabolite on lists of 243 total metabolites.</p
Quantile-quantile plot.
<p>Expected p-values assuming a uniform distribution (X-axis; expected −log10(p-value)) were compared to observed p-values (Y-axis; observed −log10(p-value)) in the continuous analysis (A) and dichotomous analysis (B) to evaluate the levels of inflation in test statistics. Expected p-values were calculated based on the uniform distribution assuming each test was independent of others.</p
Significant probes in continuous and dichotomous analysis.
<p>Pearson’s correlation test and Student’s-t test were used for continuous and dichotomous analysis, respectively. (A) From left to right, numbers in Venn diagram indicate the number of probes significant only in continuous analysis, probes significant in both continuous and dichotomous analysis, and probes significant only in dichotomous analysis by p-value cut-off of 0.01. We did not observe differences between shared genes and specific genes in terms of p-values, correlation coefficients, and fold-changes. (B) Probes significant in both analyses (154 probes) were further categorized based on the correlation coefficient and fold-change.</p
Comparison of test statistics.
<p>(A) Pearson’s correlation coefficients in the continuous analysis were compared to fold-changes in the dichotomous analysis to evaluate overall similarity in direction of changes between two analytical methods. The number in each quadrant represents the percentage of probes relative to all probes analyzed. (B) Significance levels in the continuous analysis (−log10(Pearson’s test p-value); X-axis) were compared to those in the dichotomous analysis (−log10(Student’s t-test p-value); Y-axis) in order to evaluate overall similarity in significance between two analytical methods.</p
HD CAGnome.
<p>HD CAGnome is accessible at <a href="http://chgr.partners.org/cgi-bin/cagnome.cgi" target="_blank">http://chgr.partners.org/cgi-bin/cagnome.cgi</a>.</p