21 research outputs found
Altered brain proteins at FDR<15% in Active versus Control participants.
No full textA-K) Expression of the 11 altered brain proteins at FDRFig 3A. Error bars indicate SEM. L) The 11 altered proteins were associated with 2 signaling pathways having a p value of overlap 2. The same four proteins (FGA, FGB, FGG, PLG) were associated with activation of the coagulation system (p value of overlap = 1.45 x 10−9, z = 2.00) and acute phase response signaling (p value of overlap = 1.23 x 10−6, z = 2.00). (TIF)</p
Proteomics in whole brain homogenate.
No full textProteomics was performed in surgically resected brain tissue from Active and Control participants. A) PCA in brain tissue indicated no segregation of Active and Control participants in PCA1 (p = 0.73) and with some segregation in PCA2 (p = 0.016). Clinical diagnoses (FCD, TSC) are noted as well. B) Differential expression analysis in brain tissue indicated that there were 11 significantly altered proteins in Active versus Control participants at an FDR S1 Table and S1 Fig. There were no significant proteins at FDR C) WGCNA of brain proteomics and phospho-S6 evaluated in total brain homogenate by western blot, regardless of everolimus and clinical diagnoses. There were 1109 proteins that correlated with phospho-S6 levels (P235/236, p −6, R2 = 0.87) in the M-Brown module. D) The top significantly correlated protein with P240/244 was a negative correlation with ANK2 (p = 7.92 x 10−5, R2 = 0.74) in the M-Brown module. E) Module trait correlation identified 5 significantly associated modules with phospho-S6 (p < 0.05). Modules were clustered by eigenprotein adjacency (relatedness to other modules) on the left. Name of module is indicated by “M-color.” P values are indicated for those modules with p < 0.05 correlation. Positive correlation is indicated in red and negative correlation in blue. Top module GO annotations are noted on the right (FDR < 5%, at least 5 proteins/annotation). Several modules did not have a significant GO annotation (“n.s.”).</p
Ribosomal S6 phosphorylation in whole brain homogenate.
No full textA) Representative western blot images from surgically resected brain tissue of Active participants after taking 4.5 mg/m2 everolimus for 7 days and controls. Total S6, phospho-S6 (Ser235/236), phospho-S6 (Ser240/244), and beta-actin as loading control were evaluated in 14 participants. TSC participants are indicated “*”, while all others are FCD participants. B) Quantification of total S6 relative to actin indicates variability in baseline levels from sampled brain tissue, as well as one patient with increased expression of a smaller detected band (NYU-002). C) Percentage of phospho-S6 (Ser235/236) relative to total S6 indicates an average 1.19-fold decrease when comparing all Active participants to controls (p = 0.67). The highest level was seen in NYU-004. D) Percentage of phospho-S6 (Ser240/244) relative to total S6 indicates an average 1.15-fold decrease when comparing all Active participants to controls (p = 0.66). The highest level was seen in NYU-004. Error bars indicate SEM.</p
Whole western blot images for phospho-S6 (Ser235/236).
No full textA) All cases (n = 14) were evaluated by western blot for phospho-S6 (Ser235/236) quantification on 2 blots, as depicted in Fig 1A. Bands were visualized after ECL on a BioRad ChemiDoc. Quantification was performed on bands in the red outlined box in Fiji ImageJ. One sample (NYUC001) was included on both gels to allow for normalization across blots for all samples. A’) Corresponding ladder for panel A is shown in the colorometric brightfield image. B) On the same blots, actin was evaluated after stripping the phospho-S6 (Ser235/236). B’) Corresponding ladder for panel B is shown in the colorometric brightfield image. C) On the same blots, total S6 was evaluated with no stripping (both actin and total S6 are present). C’) Corresponding ladder for panel C is shown in the colorometric brightfield image. (PDF)</p
