Journal: bioRxiv

Article Title: Dynamic Regulation OF The Chromatin Environment By Ash1L Modulates Human Neuronal Structure And Function

doi: 10.1101/2024.12.02.625500

Figure Lengend Snippet: (A) Diagram of ASH1L protein domains showing the location of the pathogenic variant E2148* (blue) in ASH1L catalytic domain and itsr associated clinical phenotypes. (B) Illustration depicts the dual SMAD inhibition protocol used to generate cortical excitatory human neurons. ( C ) ASH1L expression was quantified by qPCR using human neurons at day 35 of neuronal induction. Fold change is normalized to control. Bar represents the mean and individual measures from four independent experiments are shown for control (grey with open circles), and E2148* (light blue with solid blue circles). Samples were analyzed as a ratio of the control. Statistical analysis was conducted using unpaired t-test. **** P < 0.0001. ( D ) Representative images are shown for human neurons from control, and E2148* cultures at day 35 of neuronal induction. Neurons stained with MAP2 are shown in black and white for ease of viewing. Calibration bars represent 20µm. ( E-H ) Morphogenesis measures are shown for four independent experiments for control neurons (grey bar with open circles), and E2148* mutant neurons (light blue bars with solid dark blue circles). Individual points represent the average of 4 independent experiments, an average of 30 neurons were measured per experiment. ( E ) Mean neurite length is shown for control (n=124 neurons; 56.9 ± 2.41), and E2148* (n=118 neurons; 47.47 ± 1.99). Grouped statistical analysis was conducted using unpaired t-test, **P < 0.004. ( F ) Total neurite length is shown for control (n=124 neurons; 182.7 ± 6.39), and E2148* (n=118 neurons; 139.3 ± 4.66). Grouped statistical analysis was conducted using unpaired t-test, **** P < 0.0001. ( G ) Neuronal morphology analyzed by measuring the complexity index (see methods). Calculations were conducted after identifying outliers using the ROUT 1% method for control (n=115; 289.5 ± 18.21), and E2148* (n=112; 228.8 ± 13.42). Grouped statistical analysis was conducted unpaired t-test ** P < 0.0099. ( H ) Cell soma size was analyzed for three independent experiments by measuring the area for control (n=96; 77.67 ± 3.47), and E2148* (n=91; 69.15 ± 2.51). Statistical analysis was conducted using unpaired t-test P=0.056. ( I ) Sholl analysis was used to measure neuronal arborization. The number intersections away from the cell soma were measured every 10µm and are shown for control (open gray circles), and E2148* (solid dark blue circles) neurons from 10µm to 120µm. Statistical analysis was conducted using a mixed model effects *** P < 0.0006, and **** P < 0.0001. ( J-L ) Analysis of H3K36me2 and H3K4me3 levels on chromatin fraction for four independent experiments is shown for neurons at day 41 of neuronal induction. ( J ) Representative western blot shows H3K36me2, H3K4me3 and histone H3 for control, and E2148* neurons. H3 Histone marks were normalized to histone H3 levels for analysis. ( K ) H3K36me2 protein levels are shown for control (1± 0), and E2148* (0.67 ± 0.26). ( L ) H3K4me3 protein levels are shown for control (1± 0), and E2148* (0.68± 0.11). (K -L ) Statistical analysis was conducted using unpaired t-test *P< 0.025. Not significant P value is not shown.

Article Snippet: Primary antibody for MAP2 (Aves lab, #MAP) was added and cells were incubated overnight at 4°C, followed by secondary antibody incubation for 1 hour at room temperature using Alexa Fluor 647 (Thermo Scientific, #A-21449) at a dilution of 1:1000.

Techniques: Variant Assay, Inhibition, Expressing, Control, Staining, Mutagenesis, Western Blot

Journal: bioRxiv

Article Title: Dynamic Regulation OF The Chromatin Environment By Ash1L Modulates Human Neuronal Structure And Function

doi: 10.1101/2024.12.02.625500

Figure Lengend Snippet: ( A ) PCA plots shows biological replicates (n=4) for control (green), and E2148* (salmon) neurons RNA seq experiments. ( B ) Heatmap shows top 100 DEGs for control (green), and E2148* (salmon) neurons at day 35 (n=4 biological replicates). The top 15 DEGs are listed. ( C ) Volcano plots showing DEGs in the heterozygous E2148* mutant iPSC-derived neurons. Log 2 fold changes (LFC) gene expression (x-axis) and -log 10 adjusted P values (y-axis) generated from DESeq2 differential gene expression analysis are shown. Vertical dotted lines represent 0.58 LFC (1.5 FC) and horizontal dotted line shows adjusted P=0.05. Significant DEGs are shown in red with the top 20 labelled in the plot. ( D-F ) Functional enrichment analysis by EnrichR for biological process ( D ), cellular compartment ( E ), and molecular function ( F ) show enrichment for all DEGs, upregulated and downregulated DEGs in E2148* mutant neurons vs. control neurons. Circle size represents the number of DEGs in that category and the color represents the adjusted P value. ( G ) Correlation of gene length to fold change analyzed for all significant DEGs in E2148* (blue line) mutant neurons. Grey shade shows the variability across samples. ( H ) Analysis of gene length in upregulated (blue) and downregulated (red) DEGs for E2148* neurons. ( I ) Analysis of de novo transcription by EU click chemistry at day 41 of neuronal differentiation. Representative images of human neurons that incorporated EU (gray), stained with neuronal marker MAP2 (cyan) and nuclear marker DAPI (blue) are shown for control (top row), and E2148* (bottom row). Enlarged nuclei stained with EU is shown. Calibration bars are 20µm. ( J-K ) Measurements of EU incorporation are shown for control neurons (grey bars with open circles), and E2148* (light blue bars with solid deep blue circles) mutant neurons. Mean and standard error are shown with individual dots representing the average of individual measures for five independent experiments. ( I ) Pearsons’ correlation coefficient analysis is shown for five independent experiments for control (n=187; 0.785 ± 0.003), and E2148* (n=115; 0.746 ± 0.005) neurons. ( J ) EU nuclear intensity normalized to control is shown for five independent experiments for control (n=187; 1.017 ± 0.029), and E2148* (n=115; 0.817 ± 0.027) neurons. ( I-J ) Grouped data analyzed using unpaired t test with Welch’s correction, ****P < 0.0001. Not significant P values are not shown.

Article Snippet: Primary antibody for MAP2 (Aves lab, #MAP) was added and cells were incubated overnight at 4°C, followed by secondary antibody incubation for 1 hour at room temperature using Alexa Fluor 647 (Thermo Scientific, #A-21449) at a dilution of 1:1000.

Techniques: Control, RNA Sequencing, Mutagenesis, Derivative Assay, Gene Expression, Generated, Functional Assay, Staining, Marker

Journal: bioRxiv

Article Title: Dynamic Regulation OF The Chromatin Environment By Ash1L Modulates Human Neuronal Structure And Function

doi: 10.1101/2024.12.02.625500

Figure Lengend Snippet: (A) Representative images are shown for day 35 human neurons from control, and E2148* cultures treated for 3 days with DMSO, Tazemetostat (0.5µM) and Vorinostat (0.1µM). Neurons stained with MAP2 are shown in black and white for ease of viewing. Calibration bars represent 30µm. ( B-F ) Morphogenesis analysis is shown for at least 4 independent experiments (unless otherwise annotated) in which we measured at least 30 neurons per experiment for control (grey bar with open circles) and E2148* (light blue bars with solid dark blue circles) neurons treated with either DMSO, Tazemetostat (TAZ) or Vorinostat (VOR). Individual points represent the average of multiple independent experiments. ( B ) Total neurite length is shown as the mean (bar) with the average of individual measurements represented by the circles for: control + DMSO (n=93 neurons; 231.9 ± 7.27); control + TAZ (n=119; 184.4± 5.46); control + VOR (n=118 neurons; 227.3± 6.8); E2148* + DMSO (n=113 neurons; 163.3 ± 4.83); E2148* + TAZ (n=112; 200.5± 5.94); E2148* + VOR (n=129 neurons; 225.2± 8.38). ( C ) Mean neurite length is shown as the mean (bar) with the average of individual measurements represented by the circles for: control + DMSO (n=90 neurons; 69.86 ± 2.409); control + TAZ (n=117; 64.16± 2.04); control + VOR (n=118 neurons; 81.28± 2.75); E2148* + DMSO (n=112 neurons; 55.75 ± 1.88); E2148* + TAZ (n=111; 66.16 ± 2.47); E2148* + VOR (n=126 neurons; 76.02 ± 2.58). ( D ) Complexity index measurements were first analyzed using the “identify outliers” ROUT function in graph pad and are shown as the mean (bar) with the average of individual measurements represented by the circles for: control + DMSO (n=90 neurons; 390± 26.88); control + TAZ (n=111; 329.4 ± 22.40); control + VOR (n=116 neurons; 461.8 ± 25.45); E2148* + DMSO (n=116 neurons; 261.9 ± 18.80); E2148* + TAZ (n=105; 357.6 ± 20.83); E2148* + VOR (n=125 neurons; 458.3 ± 29.66). ( B-D ) Statistical analysis of grouped measurements was conducted using TWO-way ANOVA with Tukey’s test for multiple comparisons: * P < 0.04 ** P < 0.009, *** P < 0.0006, **** P < 0.0001. ( E ) Sholl analysis was used to measure neuronal arborization across three different treatments in the E2148* mutant neurons. The number intersections away from the cell soma were measured every 10µm and are shown for E2148* + DMSO (inverted dark blue triangles), E2148* + TAZ (open triangles), and E2148* + VOR (solid light blue triangles) neurons. Statistical analysis by TWO-way ANOVA with mixed model effects * P < 0.05, ** P < 0.009, and *** P = 0.0008. Green asterisk (E2148* +DMSO vs. E2148* + VOR), red asterisk (E2148* + DMSO vs. E2148* + TAZ). ( F ) Sholl analysis is shown to compare the most effective treatment (vorinostat) to the untreated control and E2148* mutant neurons. The number of intersections away from the cell soma were measured every 10µm and are shown for control+ DMSO (open gray circles), E2148* + DMSO (solid dark blue circles) and E2148* + VOR (half pink/light blue circles) neurons. Statistical analysis by TWO-way ANOVA with mixed model effects * P < 0.05, ** P < 0.005, *** P = 0.0005, and **** P < 0.0001. Green asterisk (E2148*+DMSO vs. Control + DMSO), red asterisk (E2148* + DMSO vs. E2148* + VOR). ( G-K ) Analysis of nuclear levels of H3K27me3 and H4K16ac in four independent experiments (unless otherwise indicated) across all treatments is shown for neurons at day 35 of neuronal induction. ( G ) Representative images of nuclear H3K27me3 (red) are shown for either DMSO (left column) or Tazemetostat (right column) treated control, or E2148* mutant neurons stained with MAP2 (cyan) and nuclei is stain with DAPI (blue). ( H ) Quantification of H3K27me3 nuclear levels measured by mean gray value is shown for all treatments. Measurements from at least 3 independent experiments with at least 30 neurons analyzed per experiment were analyzed as a group and are shown as the mean (bar) with the average of individual measurements represented by the circles for: control + DMSO (n=134 neurons; 547.4 ± 13.19); control + TAZ (n=154; 258.1 ± 10.83); control + VOR (n=101 neurons; 545.5 ± 19.07); E2148* + DMSO (n=141 neurons; 471.0 ± 10.87); E2148* + TAZ (n=140; 301.1 ± 8.03); E2148* + VOR (n=103 neurons; 539.4 ± 18.79). ( I ) Representative images of nuclear H4K16ac (red) are shown for either DMSO (left column) or Tazemetostat (right column) treated control, and E2148* mutant neurons stained with MAP2 (cyan) and nuclei is stain with DAPI (blue). ( J ) Quantification of H4K16ac nuclear levels measured by mean gray value is shown for all treatments. Measurements from at least 3 independent experiments with at least 30 neurons analyzed per experiment were analyzed as a group and are shown as the mean (bar) with the average of individual measurements represented by the circles for: control + DMSO (N= 4 experiments; n=114 neurons; 322.8 ± 12.85); control + TAZ (n=95; 360.5 ± 13.04); control + VOR (n=145 neurons; 581.6 ± 16.45); E2148* + DMSO (n=166 neurons; 270.3 ± 10.33); E2148* + TAZ (n=106; 350.4 ± 11.81); E2148* + VOR (n=158 neurons; 654.7 ± 9.49). ( H and J ) Statistical analysis of grouped measurements was conducted using TWO-way ANOVA with Tukey’s test for multiple comparisons: * P < 0.05, *** P < 0.005, *** P < 0.0005, **** P < 0.0001.

Article Snippet: Primary antibody for MAP2 (Aves lab, #MAP) was added and cells were incubated overnight at 4°C, followed by secondary antibody incubation for 1 hour at room temperature using Alexa Fluor 647 (Thermo Scientific, #A-21449) at a dilution of 1:1000.

Techniques: Control, Staining, Mutagenesis

Journal: PloS one

Article Title: Dysferlin interacts with tubulin and microtubules in mouse skeletal muscle.

doi: 10.1371/journal.pone.0010122

Figure Lengend Snippet: Figure 6. Dysferlin binds to microtubules. His-myc-dysferlin purified on Ni-NTA beads was incubated with polymerized microtubules. Reactions were resolved by SDS-PAGE stained with SimplyBlue SafeStain. Arrows point to His-myc-dysferlin, tubulin, BSA, and to MAP1&MAP2 of the microtubule-associated protein fraction (MAPF), which includes MAP2A, MAP2B, MAP1 and tau. S: Soluble phase, P: Pellet. Lane 1: Microtubules alone, lane 2: Microtubules incubated with MAPF, lane 3: Microtubules incubated with BSA, lane 4: MAPF alone, lane 5: BSA alone, lane 6: Purified His-myc- dysferlin alone, lane 7: Microtubules incubated with purified His-myc-dysferlin. doi:10.1371/journal.pone.0010122.g006

Article Snippet: BSA was used as a negative control and the microtubule binding fraction (MAPF) provided by the cytoskeleton assay kit containing MAP2A, MAP2B, MAP1 and tau as a positive control, where MAP2 constitutes 70% of MAPF.

Techniques: Purification, Incubation, SDS Page, Staining

Journal: Molecular and cellular endocrinology

Article Title: Estrogen receptor beta maintains expression of KLF15 to prevent cardiac myocyte hypertrophy in female rodents

doi: 10.1016/j.mce.2017.11.004

Figure Lengend Snippet: (a) TGFβ stimulates p38α activity, inhibited by SB2036580 or β-LGND. Bar graph is the mean±SD from 3 exps combined. *p < 0.05 vs. control, +p < 0.05 for TGFβ vs same + SB2036580 or β-LGND. (b) TGFβ inhibits KLF15 mRNA and protein in cardiomyocytes, blocked by the p38 antagonist SB2036580 (0.1μM) (c) TAK1 activating phosphorylation is stimulated by AngII or TGFβ, inhibited by β-LGND. *p<0.05 vs. control, + p<0.05 for TGFβ or AngII vs same plus β-LGND, n=3 exps. (d) TAK1 siRNA diminishes TGFβ or AngII-stimulated p38α activity. The latter was seen as phosphorylation at tyrosine182. *p<0.05 vs control, +p<0.05 for TGFβ or AngII vs same + β-LGND, n=3 exps. TAK1 siRNA validation is also shown. (e) Flow cytometry analysis of β-LGND inhibition of phospho-kinases due to cAMP/PKA. *p<0.05 for control vs. AngII-stimulated phospho-TAK1, phospho-p38α, or KLF15 proteins. +p<0.05 for AngII vs AngII + β-LGND, ++p<0.05 for AngII + β-LGND vs same + either H-89 (PKA inhibitor) or RP-8-Br-cAMP (cAMP inhibitor), n=3 exps.

Article Snippet: Additional antibodies and phospho-specific antibodies used for immuno-blots were obtained from the followings: Cell Signaling Technology (Danvers, MA) TAK1 (D94D7) (#5206), Phospho-ATF-2 (Thr71) (#9221), Phospho-TAK1 (Thr187) (#4536); Santa Cruz, Biotechnology (Dallas, TX), KLF15 (A5) (SC-271675), GAPDH (0411) (sc-47724), MYH7 (A4.951) (sc-53090), Actin (2Q1055) (sc-58673), p38 Antibody (A-20) (sc-535), phospho-p38 (Thr 180/Tyr 182) (sc-17852-R); (Boster Biological Technology, Pleasanton, CA), ACTA2 (M01072–1).

Techniques: Activity Assay, Control, Phospho-proteomics, Biomarker Discovery, Flow Cytometry, Inhibition

Journal: Molecular and cellular endocrinology

Article Title: Estrogen receptor beta maintains expression of KLF15 to prevent cardiac myocyte hypertrophy in female rodents

doi: 10.1016/j.mce.2017.11.004

Figure Lengend Snippet: AngII acting through TGFβ stimulates a TAK1-p38α kinase axis that inhibits KLF15 expression and nuclear localization of the protein. This contributes to increased gene expression and cardiomyocyte hypertrophy. ERβ acting through protein kinase A opposes TAK1-p38α activation. This restores KLF15 abundance and nuclear localization, contributing in part to inhibition of AngII-induced gene expression and cardiomyocyte hypertrophy.

Article Snippet: Additional antibodies and phospho-specific antibodies used for immuno-blots were obtained from the followings: Cell Signaling Technology (Danvers, MA) TAK1 (D94D7) (#5206), Phospho-ATF-2 (Thr71) (#9221), Phospho-TAK1 (Thr187) (#4536); Santa Cruz, Biotechnology (Dallas, TX), KLF15 (A5) (SC-271675), GAPDH (0411) (sc-47724), MYH7 (A4.951) (sc-53090), Actin (2Q1055) (sc-58673), p38 Antibody (A-20) (sc-535), phospho-p38 (Thr 180/Tyr 182) (sc-17852-R); (Boster Biological Technology, Pleasanton, CA), ACTA2 (M01072–1).

Techniques: Expressing, Gene Expression, Activation Assay, Inhibition

Journal: Molecular Biology of the Cell

Article Title: Localization and retention of p90 ribosomal S6 kinase 1 in the nucleus: implications for its function

doi: 10.1091/mbc.E11-07-0658

Figure Lengend Snippet: RSK1 phosphorylation by PDK1 is required for its nuclear translocation. (A) Schematic of phosphorylation sites on rat RSK1. (B) Top two rows, serum-starved HeLa cells were treated with and without EGF (100 nM) for 10 min and the localization of total RSK1 was monitored with anti-RSK1 antibody; 4′,6-diamidino-2-phenylindole staining shows nuclei. Bottom four rows, the PDK1 inhibitor BX795 inhibits nuclear translocation of RSK1. HeLa cells were treated as described above with and without overnight preincubation with 0.5 μM BX795. The localization of active RSK1 was monitored with anti–phospho-T573-RSK antibody. (C) BX795 inhibits phosphorylation of RSK1 on S221 and S732. Cells were treated as in B. After immunoprecipitation with anti-RSK1 antibody, Western analyses of the immune complexes were performed with anti–phospho RSK antibodies. Scale bar, 10 μm. Representative data from three independent experiments are shown.

Article Snippet: Anti–phospho-RSK1/2 (S221) from R&D Systems (Minneapolis, MN), anti–phospho-RSK (T359/S363) from Cell Signaling (Beverly, MA), anti–phospho-RSK (S380) from Epitomics (Burlingame, CA), anti–phospho-RSK (T573) from Cell Signaling, and anti–phospho-RSK S732 raised by Rockland (Gilbertsville, PA) were used.

Techniques: Phospho-proteomics, Translocation Assay, Staining, Immunoprecipitation, Western Blot