Journal: iScience

Article Title: Oxygen tension-dependent variability in the cancer cell kinome impacts signaling pathways and response to targeted therapies

doi: 10.1016/j.isci.2024.110068

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Article Snippet: Rabbit monoclonal anti-phospho-p44/42 MAPK (T202/Y204) , Cell Signaling Technology , Cat# 9101; RRID:AB_331646.

Techniques: Control, Recombinant, Gentle, Red Blood Cell Lysis, Protease Inhibitor, cDNA Synthesis, BrdU Cell Proliferation Assay, Caspase-3 Assay, RNA Sequencing, Mass Spectrometry, Transgenic Assay, TaqMan Assay, Software, Modification, Flow Cytometry, Real-time Polymerase Chain Reaction, Isolation

Journal: bioRxiv

Article Title: Estradiol modulates neuronal network hyperexcitability in select NDD risk genes

doi: 10.64898/2026.02.18.706588

Figure Lengend Snippet: A. Schematic of experimental workflow to assess impact of estradiol on baseline gene expression in scn1lab -/- larvae. B-C . Comparison of number of Gene Ontology (GO) pathways that are originally upregulated in HOM+DMSO and downregulated by estradiol ( B ) or originally downregulated in HOM+DMSO and upregulated by estradiol ( C ). Selected reversed pathways are highlighted in the bar graphs, with bars indicating -log10(FDR). Asterisk for the p-adjusted values: * <0.05,**<0.01, ***<0.001. D. Schematic of experimental workflow to assess impact of estradiol on baseline brain activity in HOM larvae. Dissected larval brains are stained with phosphorylated ERK (pERK) as a marker of active neurons and total ERK (tERK) as a pan-neuronal marker. Images undergo voxel-by-voxel division of pERK by tERK to obtain an activity ratio. Activity is mapped onto the standard zebrafish brain atlas and quantified based on a 4-region or 149-region atlas. E. Voxel-wise Z score normalized pERK/tERK values representing brain activity differences in scn1lab Δ44/Δ44 + DMSO or estradiol compared to DMSO-treated scn1lab +/+ larvae and the difference (subtraction) between the two conditions. Rescued regions from the 149-region atlas are shown. For specific rescued regions, refer to SI Fig. 7. Images are a representative slice of the axial (top) and sagittal (bottom) view. Scale bar represents Z score (red/yellow, increased in mutant; cyan/purple, decreased in mutant). F. Bar graphs showing regional differences in pERK/tERK brain activity in the rhombencephalon, diencephalon, mesencephalon, and telencephalon. G. Left: Schematic of experimental workflow to assess impact of estradiol on induced seizure activity in scn1lab -/- larvae. Right: Pentylenetetrazole (PTZ)-induced seizure activity, with and without 24 h exposure to 20 𝜇M estradiol, is measured in scn1lab -/- larval zebrafish mutants using video-tracking. Representative activity tracings of control and scn1lab -/- larvae at 5dpf before and after exposure to DMSO vehicle or 20uM estradiol and 10mM PTZ or water. Ribbon shows +/- SEM. H. Average activity 30 min before and after the addition of 10mM PTZ or water to control and scn1lab -/- larvae before and after exposure to DMSO vehicle or 20uM estradiol. scn1lab -/- + E2 + PTZ larvae show significantly decreased activity compared to scn1lab -/- + vehicle + PTZ larvae (Unpaired t-test with Welch’s correction on post values, ****p<0.0001; n=24/group). I. Interaction models assessing genotype-x-estradiol-x-PTZ effect, comparing post- vs pre-PTZ measurements. Dissection of the mutant effect (HOM vs control), estradiol effect (Estradiol vs DMSO), and PTZ effect (PTZ vs water) (i). Three-way interaction model to estimate the PTZ effect among genotype-x-estradiol groups of larvae (ii). J. Left: Schematic of experimental workflow to assess impact of estradiol on neuronal busting activity in CRISPR-engineered SCN2A +/- iGLUTs . Right: Cellular and network bursting activity, with and without exposure to acute 100nM estradiol, is measured in SCN2A +/- NGN2-iGLUTs using multielectrode array. Bar graphs show mean number of cellular bursts and network bursts in controls and SCN2A +/- iGLUTs. Unpaired t-test, cellular bursts *p=0.0415, network bursts SCN2A +/- spontaneous vs SCN2A +/- E2 *p=0.0127, SCN2A +/- spontaneous vs WT spontaneous *p=0.0450.

Article Snippet: The following antibodies and dilutions were used: pERK (Cell Signaling #4370, RRID: AB_2315112) and tERK (Cell Signaling #4696, RRID:AB_390780), 1:500.

Techniques: Gene Expression, Comparison, Activity Assay, Staining, Marker, Mutagenesis, Control, Dissection, CRISPR

Journal: bioRxiv

Article Title: Deep Invaginations of Nuclear Envelope Coordinate Spatial Organization of Chromatin in Epithelium

doi: 10.64898/2026.03.10.710762

Figure Lengend Snippet: (A) The volcano plot of the differentially expressed genes (DEGs) in mature 7 d grown epithelium in comparison to developing 2 d grown epithelium. MAPK-signaling -associated genes highlighted in red. (B) Ingenuity pathway analysis (IPA) pathway generator -derived map presenting affected nuclear mechanotransduction and NE -associated components and their downstream actors. Red and green indicate up- and down-regulation, respectively. Purple lines indicate statistically significantly affected components (Abs(log2FC)) >1 and pAdj <0.05). (C) ClusterProfiler KEGG pathway over-representation “MAPK signaling pathway” analysis of the 7 d -grown mature epithelium showing significantly affected biological processes in the 7-d grown mature epithelium in comparison to the 2 d-grown epithelium. (D) IPA pathway generator -derived map showing affected components of MAPK-signaling. Red indicates up-regulated, and green indicates down-regulated. Purple lines indicate statistically significantly affected components (Abs(log2FC)) >1 and pAdj <0.05). (E) STRING analysis of MAPK-associated DEGs in the 7 d grown epithelium, indicating functional enrichment in three clusters within interconnected networks. (F) Transcription factor (TF) motif analysis of transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) of 2 d and 7 d grown cells indicates global decreased accessibility of TF motifs, highlighting significant suppression of MAPK/ERK-associated motifs in the mature epithelium. Box-and-whiskers plots presenting (G) intracellular normalized fluorescence intensity distribution, and (H) nucleo-cytoplasmic ratio of activated phosphorylated ERK1/2 (phospho-ERK, p44/42 MAPK) at 2, 4, and 7 d post-seeding. One-way ANOVA with Dunnett’s multiple comparisons test indicates statistical significance, n=three independent biological replicates. Box-and-whisker plots represent the 25 th –75 th percentiles as boxes, the median as a line within the box, and whiskers indicating the minimum and maximum values.

Article Snippet: Active MAPK was detected by using a mouse monoclonal Ab identifying the phosphorylated p44/42 MAPK (1:400, ERK1/2, Thr202/Tyr204 [E10], #9106, Cell Signaling Technology, MA, USA).

Techniques: Comparison, Derivative Assay, Functional Assay, Next-Generation Sequencing, Fluorescence, Whisker Assay