Journal: Cell Reports Medicine

Article Title: Marine n-3 polyunsaturated fatty acids slow sleep impairment progression by regulating central circadian rhythms in type 2 diabetes

doi: 10.1016/j.xcrm.2025.102128

Figure Lengend Snippet: Effects of DHA and EPA on circadian clocks and rhythm in hypothalamic neuron cells (A–E) Effects of 100 μM DHA/EPA plus 300 μM PA on circadian oscillations of clock genes including (A) Clock, (B) Rorα, (C) Per2, (D) Bmal1, and (E) Rev-erb. The relative mRNA expressions were detected at ZT 0, 4, 8, 12, 16, 20, 24, 28, and 32 after synchronization ( n = 3 for each group, biological replicates). The scatter diagrams were fitted by Cosinor algorithm with smooth curves. Control group colored in black, 300 μM PA colored in brown, 100 μM DHA plus 300 μM PA colored in blue, and 100 μM EPA plus 300 μM PA colored in pink. Quantification of Cosinor-fitted circadian mesor, amplitude, and acrophase was expressed as mean ± SEM. Statistical differences were determined by one-way ANOVA followed by the Dunnett’s multiple comparisons test. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001. (F–I) Representative immunoblotting of clock proteins including CLOCK, REV-ERB, RORα, and BMAL1 at ZT 4, 12, and 20 after synchronization in hypothalamic neuron cells (control n = 6, other groups n = 3, biological replicates). Data were expressed as mean ± SEM. Statistical differences between PA treatment versus other groups at same time point were determined by one-way ANOVA followed by the Dunnett’s multiple comparisons test. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001. Statistical differences between same group at different time points, statistical differences were determined by one-way ANOVA followed by the Tukey’s multiple comparisons test. # p < 0.05, ### p < 0.01, and ### p < 0.001.

Article Snippet: RORα Anti-Mouse (C-7) , Santa Cruz Biotechnology , Cat# sc-518081.

Techniques: Control, Western Blot

Journal: Cell Reports Medicine

Article Title: Marine n-3 polyunsaturated fatty acids slow sleep impairment progression by regulating central circadian rhythms in type 2 diabetes

doi: 10.1016/j.xcrm.2025.102128

Figure Lengend Snippet: RORα mediates n-3 PUFA-regulated rhythmic oscillations in molecular biology (A and B) Optimal conformation of the RORα (PDB ID: 4s15 ) docking complex bound with DHA (A) and EPA (B). The RORα structure is shown as ribbon in blue while in light blue for the enlarged zoom of the active pocket. Detailed binding residues are shown as yellow sticks, and hydrophobic interactions are all shown as semitransparent gray spheres. The yellow dotted line is hydrogen bonding, measuring a distance range of 2.0–3.0 Å; a gray translucent surface indicates hydrophobic action. (C) Free energy of binding of 4s15 receptor to ligands (4DB, DHA-derivate MaR1, DHA, and EPA) was estimated with the highest score. Molecular docking estimates were performed by AutodockVina. (D–G) Effects of 100 μM DHA/EPA plus 300 μM PA on the oscillations of circadian clock genes including Clock (D), Bmal1 (E), Per2 (F), and Rev-erb (G), in RORα-KO hypothalamic neuron cells. The relative mRNA expressions were detected at ZT 0, 4, 8, 12, 16, 20, 24, 28, and 32 after synchronization, and oscillation curves were fitted by Cosinor algorithm ( n = 3 for each group, biological replicates). (H–K) Representative immunoblotting of clock proteins including (H and J) CLOCK and (I and K) REV-ERB at ZT 4, 12, and 20 after synchronization in RORα-KO hypothalamic neuron cells ( n = 3 for each group, biological replicates). For (D)–(K), data were expressed as mean ± SEM. Statistical differences between PA treatment versus other groups at same time point were determined by one-way ANOVA followed by the Dunnett’s multiple comparisons test. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001. Statistical differences between the same group at different time points; statistical differences were determined by one-way ANOVA followed by the Tukey’s multiple comparisons test. # p < 0.05, ### p < 0.01, and ### p < 0.001.

Article Snippet: RORα Anti-Mouse (C-7) , Santa Cruz Biotechnology , Cat# sc-518081.

Techniques: Binding Assay, Western Blot

Journal: Cancer cell

Article Title: The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma

doi: 10.1016/j.ccell.2018.05.002

Figure Lengend Snippet: (A) Immunoblot for BRG1, BAF155, SS18, BAF47, and GAPDH performed on Aska SS cell whole-cell extracts in shCt and shSSX conditions (using two distinct shRNAs targeting SSX). (B) Venn diagram of SS18 (left) and BAF155 (right) ChIP-seq peaks in shCt and shSSX conditions in Aska cells. (C) IPs for BRG1, BAF250A (BAF complex-specific), and BAF200 (PBAF complex-specific) using nuclear extracts from Aska cells. (D) Heatmaps of SS18, BAF155, BRG1, and BAF200 occupancy in Aska shCt and shSSX conditions over all SS18 peaks in shCt or shSSX conditions (32,077),ranked by log2(fold change) in SS18 occupancy. (E) Example SS18, BAF155, BRG1, BAF200, RNA Pol II, ChIP-seq, and RNA-seq tracks at the FOXC1 locus in Aska cells in shCt and shSSX conditions. (F) Distance to TSS graph for shCt-only (shSSX-lost), shCt-shSSX shared, and shSSX-only (shSSX-gained) SS18 peaks in Aska cells. (G) Cumulative distribution function of ChIP-seq peak widths for shCt-only, shCt-shSSX shared, and shSSX-only SS18 peaks in Aska cells, and SS18 peaks in CRL7250 cells. (H) Venn diagram of SS18 peaks in shCt and shSSX conditions in SYO1 SS cells. (I) Heatmaps of SS18 occupancy in SYO1 shCt and shSSX conditions over all SS18 peaks in shCt or shSSX conditions (17,111), ranked by log2(fold change) in SS18 occupancy. (J) Venn diagram of V5 peaks in V5-SS18 WT and V5-SS18-SSX1 expressing conditions in CRL7250 fibroblast cells. (K) Example SS18 and V5 tracks at the SOX8 and CAV1 loci in Aska and SYO1 shCt and shSSX conditions, as well as CRL7250 in V5-SS18 WT and V5-SS18-SSX1 conditions. See also Figure S1.

Article Snippet: Mouse Anti-ARID1A (BAF250A) (C-7) (IB) , Santa Cruz , Cat#sc-373784; RRID:AB_10917727.

Techniques: Western Blot, ChIP-sequencing, RNA Sequencing, Expressing

Journal: Cancer cell

Article Title: The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma

doi: 10.1016/j.ccell.2018.05.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mouse Anti-ARID1A (BAF250A) (C-7) (IB) , Santa Cruz , Cat#sc-373784; RRID:AB_10917727.

Techniques: Microarray, Recombinant, Sample Prep, Sequencing, shRNA, Control, CRISPR, Plasmid Preparation, Software

Journal: Cell reports

Article Title: Mass Cytometry Reveals Global Immune Remodeling with Multi-lineage Hypersensitivity to Type I Interferon in Down Syndrome

doi: 10.1016/j.celrep.2019.10.038

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mouse monoclonal anti-human FOXP3 (clone 259D/C7) , Fluidigm , Cat#3159028A; RRID:AB_2811088.

Techniques: Recombinant, Mass Cytometry, Software

Journal: EMBO Molecular Medicine

Article Title: ERK5 suppression overcomes FAK inhibitor resistance in mutant KRAS-driven non-small cell lung cancer

doi: 10.1038/s44321-024-00138-7

Figure Lengend Snippet: ( A ) Percentage of proliferation inhibition of A549, A427 and H460 cell lines treated with increasing doses of XMD8-92 or Seliciclib or in combination (top) 48 h after treatment and representative crystal violet-stained cells 72 h after drug treatment (bottom). The combination index (CI) showing the synergistic effect of combination of the 2 drugs is indicated; n = 3. ( B – D ) Relative quantification of Annexin V (AV) + Annexin V/PI (AV/PI)-positive cells by flow cytometry; n = 4 ( B ), colony forming capacity; n = 3 ( C ) and percentage of cell migration; n = 10 ( D ) of A549 cells treated with 10 µM XMD8-92 or Seliciclib or in combination, except for the colony formation assay in which cells were treated with 5 µM of each drug. ( E ) Immunoblot analysis of the indicated targets in A549 cells treated with the indicated doses of Seliciclib or XMD8-92 or in combination for 24 h. ( F ) Immunoblot analysis of the indicated targets in A549 cells treated with 10 µM XMD8-92 or 10 µM Seliciclib or in combination for 24 h. ( G ) Immunoblot analysis for the indicated targets in A549 cells transduced with shRNA control (pLKO.1 hygro + Tet-pLKO-puro) or a shRNA against CDK5 (Tet-pLKO-puro-shCDK5 + pLKO.1 hygro), or a shRNA against ERK5 (pLKO.1 hygro-shERK5 + Tet-pLKO-puro) or in combination (Tet-pLKO-puro-shCDK5 + pLKO.1 hygro-shERK5). After transduction and selection, cells were harvested for protein extraction 72 h after doxycycline (1 μg/mL) induction. ( H , I ) Relative cell number ( H ) and Annexin V (AV) + Annexin V/PI (AV/PI)-positive cell quantification by flow cytometry ( I ) in A549 cells treated as in ( G ) 72 h after doxycycline (1 μg/mL) induction; n = 3. Graphical data are mean ± SD. Statistical analyses were done using one-way ANOVA; n , number of biologically independent samples. .

Article Snippet: Mouse monoclonal Anti- ERK5 (C-7) (WB: 1/1000) , Santa Cruz Biotechnology , Cat# sc-398015.

Techniques: Inhibition, Staining, Quantitative Proteomics, Flow Cytometry, Migration, Colony Assay, Western Blot, Transduction, shRNA, Control, Selection, Protein Extraction

Journal: EMBO Molecular Medicine

Article Title: ERK5 suppression overcomes FAK inhibitor resistance in mutant KRAS-driven non-small cell lung cancer

doi: 10.1038/s44321-024-00138-7

Figure Lengend Snippet: ( A ) Representative bright-field microscopy images of parental vehicle-treated A549 cells (left), VS-4718 tolerant cells (VS4718-T, middle) and VS4718-T upon withdrawal of the drug for 48 h (right). To obtain the VS-4718 tolerant (VS4718-T) cells, parental cells were treated with increasing doses of VS-4718 for 4 weeks and were after that maintained in 2.5 μM of VS-4718. Scale bars: 100 μm. ( B ) Percentage of proliferation inhibition of parental and VS4718-T A549 cells treated with increasing doses of VS-4718. Cell proliferation was determined 72 h post-treatment; n = 3. ( C ) Hierarchical clustering (Pearson Correlation, average linkage) of genes with standard deviation at top 5% showing a clear separation between A549 cells treated with VS-4718 (2.5 µM) for 12 h (acute) or rendered VS-4718 tolerant as described in ( A ); n = 3. ( D ) Analysis of the TRRUST module of Metascape showing that the genes of cluster 5 are identified as transcription factor targets (colored, left) and STRING database analysis showing the possible interaction between the different transcription factors (right). ( E ) Heatmap showing the expression profile of epithelial (KRT8,18) and mesenchymal markers of A549 cells treated as in ( C ). ( F ) Immunoblot for the indicated targets in A549 cells treated as in ( A ). The VS4718-T cells were maintained with 2.5 μM VS-4718. ( G ) Immunoblot for the indicated targets in A549 cells treated as in ( A ) and maintained at 2.5 μM. ( H ) Real-time PCR showing relative mRNA levels of ERK5 in A549 cells treated as in ( C ); n = 3. ( I ) Immunoblot for the indicated targets in A549 parental, VS4718-T and VS4718-T treated with XMD8-92 (10 μM). Heatmaps in ( C , E ) display a relative color scheme across samples that uses the minimum and maximum values in each row to convert the values into a scale ranging from 0 to 1. Graphical data are mean ± SD. Statistical analyses were done using one-way ANOVA; n , number of biologically independent samples. .

Article Snippet: Mouse monoclonal Anti- ERK5 (C-7) (WB: 1/1000) , Santa Cruz Biotechnology , Cat# sc-398015.

Techniques: Microscopy, Inhibition, Standard Deviation, Expressing, Western Blot, Real-time Polymerase Chain Reaction

Journal: EMBO Molecular Medicine

Article Title: ERK5 suppression overcomes FAK inhibitor resistance in mutant KRAS-driven non-small cell lung cancer

doi: 10.1038/s44321-024-00138-7

Figure Lengend Snippet: Reagents and tools table

Article Snippet: Mouse monoclonal Anti- ERK5 (C-7) (WB: 1/1000) , Santa Cruz Biotechnology , Cat# sc-398015.

Techniques: Recombinant, Plasmid Preparation, Sequencing, shRNA, Reverse Transcription Polymerase Chain Reaction, Transfection, Western Blot, In Vitro, In Vivo, cDNA Synthesis, TUNEL Assay, Software