Journal: Genome Medicine

Article Title: A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer’s disease

doi: 10.1186/s13073-023-01206-2

Figure Lengend Snippet: Analysis of dysregulated proteins of 5xFAD brains and postmortem brains of AD patients. a Investigation of the overlap of DEPs in brains of 5xFAD mice and postmortem AD patients. Protein changes in cortical and hippocampal tissues of 8- and 5-month-old mice (DE.cortex.Age8; DE.hippo.Age5; DE.hippo.Age8) that contain Aβ aggregates (Fig. d) were compared with patient protein measurements. The amounts of DEPs are denoted analogously to Fig. a or have been abbreviated (C8, H5, H8). The human AD data were obtained from Drummond 2022 (D22, ), Johnson 2020 (J20, ), and Johnson 2022 (J22, ). The total numbers of DEPs in each dataset are indicated in brackets. In DE.cortex.Age8 and DE.hippo.Age5, the proteins present in all four data sets are depicted with gene names. b Correlation analyses of DEPs from cortical tissues of 8-month-old mice (DE.cortex.Age8) and DEPs from hippocampal tissues of 5- (DE.hippo.Age5) and 8-month-old mice (DE.hippo.Age8) with human AD patient data from Drummond 2022, Johnson 2020 and Johnson 2022 (as indicated in panel a ) were performed. The degree of correlation was assessed by Spearman correlation coefficients (r S ) and corresponding FDR-adjusted p -values (*, p < 0.05; **, p < 0.01; ***, p < 0.001). Colors denote the values of the Spearman correlation coefficients. c Example Spearman correlations and concordance representations of dysregulated proteins from 5xFAD mice (DE.cortex.Age8, DE.hippo.Age5, and DE.hippo.Age8) versus human AD patient data from Drummond 2022 along with human AD data against each other (D22 vs J22, D22 vs J20, J20 vs J22) are shown. The identifiers are denoted analogously to Figs. a and 4a. Proteins concordantly up- or downregulated in 5xFAD mice and human AD patient brains are shown in gray quadrants and marked in blue. Proteins of interest with highly significant fold-changes are indicated with gene names. Correlating but non-concordant proteins are marked in brown. d Generation of signatures for proteins concordantly dysregulated in 5xFAD mice and human AD patient brains. The heatmaps show the 15 most down (Sig-, left) or upregulated (Sig + , right) proteins. Colors denote the values of the log2 fold-changes. e Ingenuity pathway analysis (IPA) for the complete set of concordantly dysregulated proteins. The statistical significance of the association between the DEPs and the canonical pathways was measured with a right-tailed Fisher’s exact test to calculate p -values, adjusted by the Benjamini–Hochberg multiple testing correction. All analyses are based on mean values of measured intensities from five biological replicates of tg mice per age and tissue ( n = 5)

Article Snippet: Heatmaps were created with GraphPad Prism v7 showing the 15 most down (Sig-, left) and upregulated (Sig + , right) proteins (Fig. d, Additional file : Supplementary Excel File 7).

Techniques:

Journal: Pain

Article Title: Long-term neuropathic pain behaviors correlate with synaptic plasticity and limbic circuit alteration: a comparative observational study in mice

doi: 10.1097/j.pain.0000000000002549

Figure Lengend Snippet: Gene expression profile in hippocampus and PFC of sham mice at 12 months compared with the 1-month animals. (A and D) Show the heatmap summarizing the global and distinct gene expression levels across the screening sets in hippocampus (A) and PFC (D), profiled by the results of low-density TaqMan-RT-qPCR array. The analysis was performed using GraphPad Prism software (version 7.05). (B and E) Show the expression levels of the significantly ( P < 0.05) deregulated genes between sham mice at 12 months and at 1 month in hippocampus (B) and PFC (E). Data are expressed as the mean ± SD. (C) Shows the Venn diagram representing the cross-comparison of deregulated genes within the screening sets. PFC, prefrontal cortex.

Article Snippet: Heatmap was constructed using the statistical computing tool GraphPad Prism software (v7.05).

Techniques: Gene Expression, Quantitative RT-PCR, Software, Expressing, Comparison

Journal: Pain

Article Title: Long-term neuropathic pain behaviors correlate with synaptic plasticity and limbic circuit alteration: a comparative observational study in mice

doi: 10.1097/j.pain.0000000000002549

Figure Lengend Snippet: Gene expression profile comparison between SNI and sham mice coupled by brain area and injury duration. (A, C, E, and G) Show the heatmap summarizing the global and distinct gene expression levels across the screening sets in hippocampus (A) or PFC (C) of the 1-month SNI mice compared with sham animals and in hippocampus (E) or PFC (G) of the 12-month SNI mice compared with sham animals. The heatmaps were profiled based on the results of low-density TaqMan-RT-qPCR array, and the analysis was performed using GraphPad Prism software (version 7.05). (B, D, F, and H) Show the expression levels of the significantly ( P < 0.05) deregulated genes between the 1-month SNI and sham mice at hippocampal region (B) or at PFC (D) and between the 12-month SNI and sham mice at hippocampal region (F) or at PFC (H). Data are expressed as the mean ± SD. PFC, prefrontal cortex; SNI, spared nerve injury.

Article Snippet: Heatmap was constructed using the statistical computing tool GraphPad Prism software (v7.05).

Techniques: Gene Expression, Comparison, Quantitative RT-PCR, Software, Expressing