Journal: bioRxiv

Article Title: Translatome analysis reveals cellular network in DLK-dependent hippocampal glutamatergic neuron degeneration

doi: 10.1101/2024.07.10.602846

Figure Lengend Snippet: (A) Western blot validation of immunoprecipitation of HA-tagged Rpl22. (B) qRT-PCR expression of Vglut1 (glutamatergic neuron marker), Wfs1 (CA1 marker), Vgat (inhibitory neurons), Gfap (astrocytes) shows expression of transcripts expressed in glutamatergic neurons and depletion of non-glutamatergic neuron transcripts. N=3 biological replicates, data shown as fold change of expression of marker genes in immunoprecipitated glutamatergic neuron RNA relative to whole hippocampal RNA. Normalized to Gapdh expression. (C) Venn diagram showing overlap of genes with statistically significant differential translation in DLK(cKO) and DLK(OE). (D,E) Heatmaps of significant genes from DLK(cKO) and DLK(OE). Columns represent individual mice expression levels; rows represent individual genes with the right-hand labels showing which dataset the gene was found to be statistically significant in. Data were normalized by row, with color keys shown above the heatmap. (F,G,H,I) Pie charts show expression of differentially expressed genes based on adult, endogenous expression patterns in the Allen Mouse Brain Atlas in situ data. (F,H) Upregulated, or (G,I) downregulated genes when DLK expression is (F,G) increased or (H,I) conditionally knocked out are categorized based on expression patterns in CA1, CA3, and DG in dorsal hippocampus. (J) Sunburst plot shows significant enrichment for differentially expressed genes from DLK(cKO) relating to the synapse. (K) Pathway analysis of expression data for mice with increased DLK compared to control. Nodes represent sets of genes involved in pathways, with size dependent on the number of genes in the pathway. Nodes are clustered in shaded circles based on related pathways. All pathways shown have q-value (false discovery rate <0.05). Red represents pathways enriched in mice with increased DLK. Blue indicates pathways downregulated in mice with increased DLK.

Article Snippet: Gene expression patterns of differentially translated genes were evaluated using Allen Mouse Brain Atlas in situ data from P56 mice, and supplemented with data from through the Single cell portal from the Broad Institute or data from , adolescent data through mousebrain.org when no in situ data was available or when expression was weak.

Techniques: Western Blot, Biomarker Discovery, Immunoprecipitation, Quantitative RT-PCR, Expressing, Marker, In Situ, Control

Journal: bioRxiv

Article Title: Translatome analysis reveals cellular network in DLK-dependent hippocampal glutamatergic neuron degeneration

doi: 10.1101/2024.07.10.602846

Figure Lengend Snippet: (A) Volcano plot showing RiboTag analysis of gene expression in Vglut1 Cre/+; H11-DLK iOE/+ ;Rpl22 HA/+ vs Vglut1 Cre/+ ;Rpl22 HA/+ (age P15). 260 genes showing differential expression with adjusted p-values < 0.05 are shown in red. Names of genes with p<1E-10 are labeled. (B) Volcano plot showing RiboTag analysis of genes in Vglut1 Cre/+ ;DLK(cKO) fl/fl ;Rpl22 HA/+ vs Vglut1 Cre/+ ;Rpl22 HA/+ (age P15). 36 genes showing differential expression with adjusted p-values < 0.05 are shown in blue. Names of genes with p<1E-10 are labeled. (C) Rank-rank hypergeometric overlap comparison of gene expression in DLK(iOE) and DLK(cKO) datasets shows enrichment of similar genes when DLK is low or high. Color represents the -log transformed hypergeometric p-values (blue=weaker p-value, red=stronger p-value). (D,E) Gene ontology (GO) analysis of significantly upregulated or downregulated genes, respectively, when DLK expression is increased in hippocampal glutamatergic neurons. Colors correspond to P-values. Circle size represents fold enrichment for the GO term, with number on X position showing # of significant genes included in the GO term. (F) SynGO sunburst plot shows significant enrichment for differentially expressed genes when DLK expression is increased in hippocampal glutamatergic neurons. (G,H) Pie charts show distribution of synaptic genes whose expression exhibits dependency when DLK expression is increased in hippocampus, based on in situ data in CA1, CA3, and DG in dorsal hippocampus (P56) in the Allen Mouse Brain Atlas.

Article Snippet: Gene expression patterns of differentially translated genes were evaluated using Allen Mouse Brain Atlas in situ data from P56 mice, and supplemented with data from through the Single cell portal from the Broad Institute or data from , adolescent data through mousebrain.org when no in situ data was available or when expression was weak.

Techniques: Gene Expression, Quantitative Proteomics, Labeling, Comparison, Transformation Assay, Expressing, In Situ

Journal: Science Advances

Article Title: Crossing nerve transfer drives sensory input–dependent plasticity for motor recovery after brain injury

doi: 10.1126/sciadv.abn5899

Figure Lengend Snippet: ( A ) Schematic of PRV-EGFP injection into four forelimb muscles innervated by BP (including biceps, triceps, flexors, and extensors muscle) on the impaired (right) side at 12 weeks after surgery (top) and the strategy of EGFP + cortical neurons mapping (bottom). ( B ) Schematic of BP nerves in different groups (top). Fluorescence images showing EGFP + neurons (green) in the different cortical regions of the intact hemisphere traced from the impaired forelimb in all four groups (middle). Scale bars, 200 μm. Plotting of EGFP + neurons traced from the impaired forelimb (bottom). ( C ) Schematic of dorsal view of the right sensorimotor cortex. Scale bar, 1 mm. Colors indicate conventional functional regions: orange, M1, primary motor cortex; yellow, M2, secondary motor cortex; green, S1, primary sensory cortex, based on Allen Brain Atlas. Forelimb-related motor areas (RFA and CFA) are schematically shown as dotted circles ( , , ). ( D and E ) The percentage of EGFP + neurons distributed in (C) of the forelimb-related motor areas (D) and the different functional cortical regions (E) in three groups at 12 weeks after surgery ( n = 3 for unlesioned group, n = 4 for other groups). * P < 0.05 and ** P < 0.01, unpaired t test. ( F ) The percentage of EGFP + neurons distributed in (C) of the different functional cortical regions in three CC7 related groups at 12 weeks after surgery ( n = 4 for CC7 and n = 3 for other groups). * P < 0.05 and ** P < 0.01, unpaired t test. ( G ) Schematic of distribution pattern of EGFP + neurons in the intact sensorimotor cortex tracing from the impaired forelimb at 12 weeks after surgery. The impaired forelimb-related motor areas are schematically shown as orange hollow circles, and the orange solid circle represents the most significantly increased region in the CC7 group comparing to the TBI group.

Article Snippet: After aligning these brain slices to the corresponding sections of the Allen Mouse Brain Atlas (2015 Allen Institute for Brain Science, Allen Brain Atlas API, available at brain-map.org/api/index.html ) based on several reference points, we chose an appropriate threshold to binarize these images while preserving the real fluorescent signal as much as possible.

Techniques: Injection, Muscles, Fluorescence, Functional Assay