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: bioRxiv

Article Title: GPCR endocytosis rewires neuronal gene expression and cellular architecture

doi: 10.1101/2025.08.26.672159

Figure Lengend Snippet: (A) Left : Schematic of the workflow for generation of human iPSC-derived cortical neurons. Right : Fixed cell fluorescence microscopy staining of iNeuron cultures (DIV21) with antibodies for the cortical marker, NGN2 (green), and neuronal marker, MAP2 (red). (B) Representative images of neurons treated with vehicle (no drug, ‘ND’) or 1 μM Isoproterenol (Iso) for 2 h, fixed and stained with antibody for MAP2 three days later (left) ; quantification of numbers of crossings by Sholl analysis (right) . Data are mean of n = 21–25 cells from 3 independent experiments. (C) Left: Representative images of neurons stained for vGLUT1 as presynaptic marker (green) and PSD95 as postsynaptic marker (red). Right: Quantification of synaptic pairs based on colocalization analysis of vGLUT1/PSD95 puncta per 35 μ m . Neurons were treated with vehicle (‘ND’) or 1 μM Isoproterenol (‘Iso’) for 24 h. Data are mean of n = 12 cells from 3 independent experiments. Error bars represent standard error of the mean. **** = p < 0.0001 by unpaired Student’s t test. Scale bars, 50 μm in (B) and 10 μm in (C) .

Article Snippet: Chicken anti-MAP2 monoclonal antibody (Phosphosolutions, Cat #1099-MAP2), rabbit anti-NGN2 polyclonal antibody (Invitrogen Cat #PA5–78556), guinea pig anti-VGLUT1 polyclonal antibody (Millipore, Cat #AB5905), rabbit anti-PSD95 polyclonal antibody (Abcam, Cat #AB18258) were used at 1:1,000 for immunofluorescent staining.

Techniques: Derivative Assay, Fluorescence, Microscopy, Staining, Marker

Journal: bioRxiv

Article Title: GPCR endocytosis rewires neuronal gene expression and cellular architecture

doi: 10.1101/2025.08.26.672159

Figure Lengend Snippet: (A-B) Detection of active β2AR/Gαs on endosomal vesicles. Left : Representative confocal images of neurons expressing Flag-tagged receptor (red) and GFP-tagged conformational biosensors for detection of active β2AR (Nb80, green) (A) and Gαs (Nb37, green) (B) . 1 μM Isoproterenol (Iso) was added at t=0. Right : Line scan analyses of colocalization between the β2AR and the biosensor. Yellow line: line scan analysis of gray value in each channel. Arrows indicate colocalization. (C) Endocytosis is required for cAMP accumulation. Neurons were pretreated with vehicle (DMSO) or 30 μM Dyngo-4a for 30 min, then stimulated with 1 μM Iso for 5 min, lysed and cAMP levels were measured using an ELISA assay. Data are mean of n = 3 independent experiments. (D-E) Analyses of dendritogenesis and synapse formation. Representative images are shown for each condition. Neurons were fixed and stained for MAP2 (D) or vGLUT1/PSD95 (E) . Neurons were pretreated with vehicle (DMSO) or 30 μM Dyngo-4a for 30 min, then stimulated with 1 μM Iso or 100 μM cAMP analog (8Br-cAMP). Quantification of number of crossings by Sholl analysis (D) and synaptic pairs (E) is shown. Data are mean of n = 18–25 cells in (D) , n = 9–12 (E) from 2–3 independent experiments. Error bars represent standard error of the mean. **** = p < 0.0001, *** = p < 0.001, ** = p < 0.01, * = p < 0.05 by two-way ANOVA with Sidak correction in (C) , one-way ANOVA with Dunnett correction in (D-E) . ND = no drug; Veh = vehicle. Scale bars, 10 μm in (A), (B), (E) and 50 μm in (D) .

Article Snippet: Chicken anti-MAP2 monoclonal antibody (Phosphosolutions, Cat #1099-MAP2), rabbit anti-NGN2 polyclonal antibody (Invitrogen Cat #PA5–78556), guinea pig anti-VGLUT1 polyclonal antibody (Millipore, Cat #AB5905), rabbit anti-PSD95 polyclonal antibody (Abcam, Cat #AB18258) were used at 1:1,000 for immunofluorescent staining.

Techniques: Expressing, Enzyme-linked Immunosorbent Assay, Staining

Journal: bioRxiv

Article Title: GPCR endocytosis rewires neuronal gene expression and cellular architecture

doi: 10.1101/2025.08.26.672159

Figure Lengend Snippet: (A-B) PKA and mTOR are required for β2AR-induced neuronal morphogenesis. Representative images of dendritogenesis and synapse formation analyses are shown. Neurons were fixed and stained for MAP2 (A) or vGLUT1/PSD95 (B) . Neurons were pretreated with vehicle (DMSO), 10 μM H89 or 100 nM Torin for 30 min, then stimulated with 1 μM Iso. Quantification of number of crossings by Sholl analysis (A) and synaptic pairs (B) is shown. Data are mean of n = 13–17 cells in (A) and n = 10 cells in (B) from 2–3 independent experiments. (C-D) Endosomal β2AR signaling and PKA are required for mTOR activation. Neurons pretreated with vehicle (DMSO), 10 μM H89, 30 μM Dyngo-4a or 100 nM Torin for 30 min, then stimulated with 1 μM Iso for 30 min. Representative Western blots of 4E-BP1 phosphorylation (Thr37/46) are shown. (E) Model: Endosomal GPCR signaling elicits morphogenesis through transcriptional and translational changes that together boost the cell’s protein synthesis capacity to provide key structural effectors. Error bars represent standard error of the mean. **** = p < 0.0001 by one-way ANOVA with Dunnett correction. ND = no drug; Veh = vehicle. Scale bars, 50 μm in (A) and 10 μm in (B) .

Article Snippet: Chicken anti-MAP2 monoclonal antibody (Phosphosolutions, Cat #1099-MAP2), rabbit anti-NGN2 polyclonal antibody (Invitrogen Cat #PA5–78556), guinea pig anti-VGLUT1 polyclonal antibody (Millipore, Cat #AB5905), rabbit anti-PSD95 polyclonal antibody (Abcam, Cat #AB18258) were used at 1:1,000 for immunofluorescent staining.

Techniques: Staining, Activation Assay, Western Blot, Phospho-proteomics

Journal: Oxidative Medicine and Cellular Longevity

Article Title: The Role of the miR-548au-3p/CA12 Axis in Tracheal Chondrogenesis in Congenital Pulmonary Airway Malformations

doi: 10.1155/2023/6428579

Figure Lengend Snippet: Identification of DEGs involved in the pathogenesis of CPAM. (a) Flowchart of the study design and samples at each stage of analysis. (b) Scatterplot of mRNA expression variation between diseased CPAM and normal tissues. (c) Hierarchical cluster of gene expression profiles from microarray assays. Expression of CA12, LONRF3, MAP2, THBS1, and PPID at mRNA (d) and protein (e) levels in lung tissues from CPAM and adjacent normal tissues. ∗∗∗ p < 0.001, compared with normal.

Article Snippet: Primary antibodies for this study were specific for CA12 (Boster, Cat. No. A04063, 1 : 1000), LONRF3 (GeneTex, Cat. No. GTX112150, 1 : 2000), MAP2 (Boster, Cat. No. A01201, 1 : 2000), THBS1 (Boster, Cat. No. PB0471, 1 : 2000), PPID, E-cadherin (Beyotime, Cat. No. AF6759, 1 : 1000), N-cadherin (Beyotime, Cat. No. AF5237, 1 : 800), aggrecan (Abcam, Cat. No. ab3778, 1 : 1000), Col2A1 (Boster, Cat. No. A00517, 1 : 2000), MMP13 (Proteintech, Cat. No. 18165-1-AP, 1 : 3000), ADAMTS4 (Proteintech, Cat. No. 11865-1-AP, 1 : 600), and GAPDH (Abcam, Cat. No. ab9485, 1 : 2000).

Techniques: Expressing, Gene Expression, Microarray

Journal: Journal of Dental Sciences

Article Title: Overexpression of sprouty 1 protein in human oral squamous cell carcinogenesis

doi: 10.1016/j.jds.2020.07.013

Figure Lengend Snippet: Western blot analyses: phosphor-ERK and total-ERK in human oral cancer cell lines as compared with a primary culture of normal oral mucosa (HOK). Upregulation of phosphor-ERK (normalized to total-ERK) in OECM1 and Ca922 cell lines as compared with HOK, and a slightly decreased expression in SAS as compared with HOK. Results were quantified using densitometric analysis, normalized to the level of β-actin, and expressed as a fold change relative to the normal oral mucosa. Bars represent means ± standard deviation of the mean (∗ P < 0.05). A representative result of three independent experiments is shown.

Article Snippet: Further, samples were analyzed using 10% SDS-PAGE (Sigma-Aldrich) gels, and the proteins were transmitted onto a PVDF membrane (Sigma-Aldrich) using Bio-Rad's transblot with primary antibodies against phosphor-ERK (Boster Biological Technology, CA, USA; Cat. No. P00104; 1:1000) and total-ERK (Boster Biological Technology; Cat. No. P00104; 1:1000), with species specificity for human tissues and an observed molecular weight of 42–44 kDa; and β-actin (Sigma-Aldrich; 1:1000), followed by horseradish peroxidase (HRP)-conjugated secondary antibodies (Sigma-Aldrich; 1:5000).

Techniques: Western Blot, Expressing, Standard Deviation