solvent control dmso  (MedChemExpress)

Journal: Cancer Communications

Article Title: Intranuclear paraspeckle‐circular RNA TACC3 assembly forms RNA‐DNA hybrids to facilitate MASH‐related hepatocellular carcinoma growth in an m 6 A‐dependent manner

doi: 10.1002/cac2.70061

Figure Lengend Snippet: circTACC3 m 6 A modification is associated with its intracellular localization. (A) Representative image of H&E staining of MASH‐related HCC tumor and paired peritumoral normal tissue derived organoids with relatively low (#1) and high (#2) circTACC3 expression, treated with or without PA + OA. (B) 3D fluorescence scanning of 3‐OH BrDU probe (green), anti‐Ki‐67 antibody (magenta), and DAPI (blue) indicated tissue derived organoids, treated with or without PA + OA; maximum projection of signals is shown. (C‐D) Assays of fluorescence staining with the 3‐OH BrDU probe were conducted on the cell lines with different nuclear circTACC3 level (C, n = 6) and circTACC3 knockout cell strains or negative controls (D, n = 9). The numbers on the Y‐axis represent the apoptotic rate normalized to baseline of 1. ** P < 0.01; *** P < 0.001; NS , not significant. (E) MeRIP assay shows an enrichment of m 6 A‐modified circTACC3 in cytoplasmic and nuclear fraction of HCCLM3 cells. (F) Representation of predicted m 6 A modification motif of circTACC3 (predicted using the SRAMP website). (G) Absolute quantitative RT‐qPCR of m 6 A RNA shows m 6 A modification ratio of intra‐nuclear circTACC3 in the individual motif scale. (H) The m 6 A modification levels of circTACC3 were evaluated by MeRIP in m 6 A inhibitor treated group compared to control (DMSO) group, and in PA + OA treated group compared to control (Mock) group, respectively ( n = 3). *** P < 0.001. (I) Nucleo‐plasmic fractionation to evaluate circTACC3 expression after indicated treatment ( n = 4). *** P < 0.001. (J) 3D‐FISH conducted on MASH‐related HCC tumor tissue derived organoids demonstrates the 3D distribution of circTACC3 (red) in nuclei (blue). (K) H&E staining of MASH‐related HCC tumor tissue derived organoids treated with PA + OA and/or m 6 A intervention. Abbreviations: PA, palmitic acid; OA, oleic acid; T, tumor tissues; PT, peritumoral normal tissue; H&E, hematoxylin and eosin; MeRIP, methylated RNA immunoprecipitation; m 6 A, N6‐methyladenosine; NAS, Non‐alcoholic fatty liver disease activity score; SAH, S‐adenosylhomocysteine; DAA, 3‐deazaadenosine; FISH, fluorescence i n situ hybridization.

Article Snippet: STM2457, S‐adenosylhomocysteine (SAH), 3‐deazaadenosine (DAA) or the solvent control DMSO (v/v = 1/1000, #HY‐Y0320, MedChemExpress, NJ, US) was added on Day 4.

Techniques: Modification, Staining, Derivative Assay, Expressing, Fluorescence, Knock-Out, Quantitative RT-PCR, Control, Fractionation, Methylation, RNA Immunoprecipitation, Activity Assay, Hybridization

Journal: Nucleic Acids Research

Article Title: p53 reveals principles of chromatin remodeling and enhancer activation

doi: 10.1093/nar/gkaf465

Figure Lengend Snippet: p53 is a pioneer factor that increases DNA accessibility. ( A ) ATAC-seq was performed on four biological replicates of Nutlin-3a and DMSO control-treated MCF-7 cells. Accessible sites were identified by peak calling, and their differential accessibility was assessed. ( B ) Enrichment of transcription factor binding sites that overlap sites with increased (left) or decreased (right) accessibility upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) The presence (open) or absence (closed) of an ATAC-seq peak has been assessed at 7705 recurrent p53 binding sites, and changes between the Nutlin-3a and DMSO control conditions are displayed. ( D ) p53 ChIP-seq and ATAC-seq signals are displayed for the groups identified in panel (C). Regions sorted by ATAC-seq signal. Genome browser images displaying p53 ChIP-seq and ATAC-seq data at a p53 binding site ( E ) that became accessible and ( F ) that remained inaccessible upon Nutlin-3a treatment. The predicted p53RE is highlighted. p53 ChIP-seq and nucleosome-free ATAC-seq data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS according to library size and accessible DNA background.

Article Snippet: Cells were treated with Dimethylsulfoxid (DMSO) solvent control (0.15%; Carl Roth, Karlsruhe, Germany) or Nutlin-3a (10 μM; MedChemExpress, Monmouth Junction, NJ, USA) for 24 h.

Techniques: Control, Binding Assay, ChIP-sequencing

Journal: Nucleic Acids Research

Article Title: p53 reveals principles of chromatin remodeling and enhancer activation

doi: 10.1093/nar/gkaf465

Figure Lengend Snippet: p53 establishes enhancers. ( A ) p53 binding sites were sorted by local chromatin state (promoter, enhancer, transcription, quiescent). In addition, they were sorted by the presence (open) or absence (closed) of an ATAC-seq peak in Nutlin-3a and DMSO control conditions. ( B ) CUT&Tag for H3K4me1 and H3K27ac was performed on two biological replicates of Nutlin-3a and DMSO control-treated MCF-7 cells. H3K4me1, H3K27ac, ATAC-seq, and p53 ChIP-seq signals are displayed for p53 binding sites that were closed in the DMSO control condition and open ( C ) or closed ( D ) in the Nutlin-3a treatment condition. Regions were sorted by average signal and p53 binding sites located in promoters were removed for visualization purposes because of the small group size and different signal scales. ( E ) p53 occupancy (CPM) at p53 binding sites in the different groups. Significance determined using a two-tailed Kruskal–Wallis test. *** P -value <.001.

Article Snippet: Cells were treated with Dimethylsulfoxid (DMSO) solvent control (0.15%; Carl Roth, Karlsruhe, Germany) or Nutlin-3a (10 μM; MedChemExpress, Monmouth Junction, NJ, USA) for 24 h.

Techniques: Binding Assay, Control, ChIP-sequencing, Two Tailed Test

Journal: Nucleic Acids Research

Article Title: p53 reveals principles of chromatin remodeling and enhancer activation

doi: 10.1093/nar/gkaf465

Figure Lengend Snippet: p53-induced transcription correlates with chromatin remodeling and requires high p53 abundance. ( A ) CAGE-seq was performed on four biological replicates of Nutlin-3a and DMSO control-treated MCF-7 cells. Significantly differentially regulated TSSs were identified. ( B ) Enrichment of transcription factor binding sites at sites with increased (left) or decreased (right) TSS activity upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) Comparison of changes in TSS activity (CAGE-seq) and DNA accessibility (ATAC-seq) for all TSSs in accessible DNA regions (determined by ATAC-seq peaks) upon Nutlin-3a treatment. ( D ) Subsets of TSSs/accessible sites that overlap with p53 (top panel), E2F4 (middle panel), and RFX7 binding sites (bottom panel). ( E ) p53 ChIP-seq, ATAC-seq, H3K4me1, and H3K27ac signals at p53 binding sites located in promoter regions. Subgroups were determined by overlaps with an induced TSS (log 2 FC > 0.5), uninduced TSS (log 2 FC < 0.5), and no TSS. Regions sorted by H3K27ac signal. ( F ) Comparison of changes in local transcription (CAGE-seq) and p53 occupancy (CPM from ChIP-seq). Significance determined by two-tailed Spearman correlation. Sigmoidal fit obtained best r 2 . ( G ) The fraction of promoter p53 binding sites with a canonical p53RE, noncanonical p53RE, and no p53RE.

Article Snippet: Cells were treated with Dimethylsulfoxid (DMSO) solvent control (0.15%; Carl Roth, Karlsruhe, Germany) or Nutlin-3a (10 μM; MedChemExpress, Monmouth Junction, NJ, USA) for 24 h.

Techniques: Control, Binding Assay, Activity Assay, Comparison, ChIP-sequencing, Two Tailed Test

Journal: Nucleic Acids Research

Article Title: p53 reveals principles of chromatin remodeling and enhancer activation

doi: 10.1093/nar/gkaf465

Figure Lengend Snippet: p53 preferentially directs transcription initiation to the p53RE and other sites within 100 bp. ( A ) Positional p53 motif enrichment relative to the CAGE-seq-detected TSS (CTSS) identified by HOMER2. The density of CTSSs at ±200 bp around canonical p53REs of p53 binding sites in ( B ) Nutlin-3a and DMSO control samples and ( C ) the Nutlin-3a data separated by EpiMap-derived chromatin states. ( D ) Genome browser images displaying CAGE-seq data among p53 ChIP-seq, ATAC-seq, and CUT&Tag (H3K4me1 and H3K27ac) data at two p53 binding sites. The predicted p53RE is highlighted. p53 ChIP-seq, nucleosome-free ATAC-seq, and CUT&Tag data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS. CTSSs were coverage normalized. ( E ) Dynamic p53 binding is required for Pol II initiation after its recruitment to the edges of nucleosome-depleted regions.

Article Snippet: Cells were treated with Dimethylsulfoxid (DMSO) solvent control (0.15%; Carl Roth, Karlsruhe, Germany) or Nutlin-3a (10 μM; MedChemExpress, Monmouth Junction, NJ, USA) for 24 h.

Techniques: Binding Assay, Control, Derivative Assay, ChIP-sequencing

Journal: Journal of the Endocrine Society

Article Title: Riluzole Suppresses Growth and Enhances Response to Endocrine Therapy in ER+ Breast Cancer

doi: 10.1210/jendso/bvad117

Figure Lengend Snippet: Growth suppression of ER+ breast cancer cell lines by riluzole. A, Cells seeded in 96-well plates were treated with the indicated concentrations of riluzole (RIL, 33nM to 100μM) or DMSO control for 7 to 8 days prior to staining with crystal violet. Data are presented as mean % growth ± standard error of the mean (SEM) of % growth (vehicle = 100%) for 5 or 6 technical replicates and represent 2 to 4 independent biological assays. The dotted line box indicates data re-graphed in panel B. Data were analyzed by nonlinear regression ([inhibitor] vs normalized response), yielding the following IC 50 [M] estimates: SUM44, 1.27e-4; LCCTam, 2.13e-5; MM134, 2.73e-5; MM134 LTED, 1.209e-5; MCF7, 1.09e-5; LCC9, 2.23e-5; MCF10A, 4.33e-5. B, Relative response to 10μM RIL re-graphed from panel A (dotted line box). Data are presented as median % growth with upper/lower quartiles of % growth (vehicle = 100%) for 5 to 6 technical replicates and represent 2 to 4 independent biological assays. For the SUM44/LCCTam, MM134/MM134 LTED, and MCF7/LCC9 cell line pairs, data were compared by the Mann-Whitney test. ** P = .002, ** P = .0043, and * P = .024 respectively. Dashed lines denote 50% (panels A and B) and 100% growth (panel B).

Article Snippet: PDEs were treated with 100nM fulvestrant, 10μM riluzole, the combination, or solvent control (DMSO) for 48 hours before formalin fixation, paraffin embedding, sectioning, and staining for PCNA (1:1000, Santa Cruz Biotechnology Cat# sc-56, RRID:AB_628110), cleaved caspase 3 (1:300, Cell Signaling Technology Cat# 9661, RRID:AB_2341188), and Ki67 (1:500, Abcam Cat# ab16667, RRID:AB_302459).

Techniques: Control, Staining, MANN-WHITNEY

Journal: Journal of the Endocrine Society

Article Title: Riluzole Suppresses Growth and Enhances Response to Endocrine Therapy in ER+ Breast Cancer

doi: 10.1210/jendso/bvad117

Figure Lengend Snippet: Riluzole induces a histologic subtype-associated cell cycle arrest (A-D, ILC; E-F, IDC; G, nontransformed cell control). Cells seeded in 6-well plates were treated with 10μM riluzole or DMSO control (vehicle, Veh) for the indicated times prior to collection, fixation, staining, and cell cycle analysis. Data are presented as mean % cells ± SD for 3 or 4 independent biological assays and analyzed by two-way ANOVA followed by either Sidak's (single time point) or Dunnett's (multiple time points) multiple comparisons tests. SUM44: * P = .018. LCCTam: **** P < .0001. MM134: * P = .011. MM134 LTED: * P = .05. MCF7: **** P < .0001. LCC9: * P = .015. MCF10A: not significant.

Article Snippet: PDEs were treated with 100nM fulvestrant, 10μM riluzole, the combination, or solvent control (DMSO) for 48 hours before formalin fixation, paraffin embedding, sectioning, and staining for PCNA (1:1000, Santa Cruz Biotechnology Cat# sc-56, RRID:AB_628110), cleaved caspase 3 (1:300, Cell Signaling Technology Cat# 9661, RRID:AB_2341188), and Ki67 (1:500, Abcam Cat# ab16667, RRID:AB_302459).

Techniques: Control, Staining, Cell Cycle Assay

Journal: Journal of the Endocrine Society

Article Title: Riluzole Suppresses Growth and Enhances Response to Endocrine Therapy in ER+ Breast Cancer

doi: 10.1210/jendso/bvad117

Figure Lengend Snippet: Riluzole inhibits phosphorylation of prosurvival signaling molecules and Fak/Src kinases. A, Cells seeded in 6-well plates were treated with 10μM riluzole or DMSO control (vehicle, Veh) for 2 days prior to collection, lysis, and processing, then assayed using the Human Phospho-Kinase Proteome Profiler TM Array. A ratio of background-corrected intensity values for targets (phospho-kinase spots) to references (control spots) was created for each condition (DMSO and riluzole) within each cell line. Black squares indicate absence of the indicated phospho-antibody from the array used for that cell line pair. Data are presented as the geometric mean of the riluzole: DMSO ratio for 2 technical replicates from a single experiment. B, SUM44, and LCCTam cells seeded in 6-well plates were treated with 10μM riluzole or DMSO control for several time points (6,12, 24, and 48 hours). Cells were collected, lysed, and Western blot analysis was performed to test for expression and phosphorylation of Fak Y397. The data are presented as images showing expression levels. C, Quantification analysis of Fak and P -Fak protein band density from Western blot in . D, MM134, and MM134 LTED, cells seeded in 6-well plates were treated with 10μM riluzole or DMSO control for 48 hours. Cells were collected, lysed, and Western blot analysis was performed to test for expression of Fak, as well as expression and phosphorylation of Yes Y426. E, Quantification analysis of Fak, Yes, and P -Yes protein band density from Western blot in .

Article Snippet: PDEs were treated with 100nM fulvestrant, 10μM riluzole, the combination, or solvent control (DMSO) for 48 hours before formalin fixation, paraffin embedding, sectioning, and staining for PCNA (1:1000, Santa Cruz Biotechnology Cat# sc-56, RRID:AB_628110), cleaved caspase 3 (1:300, Cell Signaling Technology Cat# 9661, RRID:AB_2341188), and Ki67 (1:500, Abcam Cat# ab16667, RRID:AB_302459).

Techniques: Phospho-proteomics, Control, Lysis, Western Blot, Expressing

Journal: Journal of the Endocrine Society

Article Title: Riluzole Suppresses Growth and Enhances Response to Endocrine Therapy in ER+ Breast Cancer

doi: 10.1210/jendso/bvad117

Figure Lengend Snippet: Riluzole can induce apoptosis and ferroptosis, and it alters expression of glutamate transporters and metabolic enzymes. A, Cells seeded in 6-well plates were treated with 10μM riluzole or DMSO control (vehicle, Veh) for 2 days prior to staining with Annexin V and PI. The percent of live cells (PI − , annexin V − ) and early apoptotic (PI − , annexin V + ) cells are shown. Data are presented as mean % cells ± SD for 3 (SUM44) or 4 (LCCTam) independent biological assays and analyzed by two-way ANOVA followed by Sidak's multiple comparisons test (* P = .021, ** P = .04 (live) and ** P = .011). B and C, SUM44 and LCCTam (B), and MM134 and MM134 LTED (C), cells seeded in 6-well plates were treated with 10μM riluzole or DMSO control for several time points (6,12, 24, and 48 hours). Cells were collected, lysed, and Western blot analysis was performed to test for expression of SLC1A5, SLC3A2, SLC7A11, GLUD1, and GPX4. The data are presented as images showing expression levels. D, SUM44 and LCCTam cells were seeded in 6-well plates. Twenty-four hours later, cells were treated with control (DMSO), riluzole (10μM), or a combination of riluzole and ferrostatin-1 (10 uM). 24 hours after treatment, the cells were collected, stained with trypan blue, and counted. Data are presented as mean ± SD of the ratio of the cell number of the treatment groups relative to the control for 3 or 4 independent biological assays and analyzed by two-way ANOVA followed by Tukey's multiple comparison test (SUM44, [** P = .005, * P = .016]; LCCTam, [** P = .002, * P = .043]). E, SUM44, and LCCTam cells seeded in 6-well plates were treated with control (DMSO), riluzole (10µM), or a combination of riluzole and ferrostatin-1 (10µM) for 48 hour. After treatment, cells were collected, lysed, and Western blot analysis was performed to test for expression of the malondialdehyde (MDA) byproduct of lipid peroxidation, and GPX4. The data are presented as images showing expression levels.

Article Snippet: PDEs were treated with 100nM fulvestrant, 10μM riluzole, the combination, or solvent control (DMSO) for 48 hours before formalin fixation, paraffin embedding, sectioning, and staining for PCNA (1:1000, Santa Cruz Biotechnology Cat# sc-56, RRID:AB_628110), cleaved caspase 3 (1:300, Cell Signaling Technology Cat# 9661, RRID:AB_2341188), and Ki67 (1:500, Abcam Cat# ab16667, RRID:AB_302459).

Techniques: Expressing, Control, Staining, Western Blot, Comparison

Journal: Journal of the Endocrine Society

Article Title: Riluzole Suppresses Growth and Enhances Response to Endocrine Therapy in ER+ Breast Cancer

doi: 10.1210/jendso/bvad117

Figure Lengend Snippet: Additive suppression of ER+ breast cancer cell line growth by riluzole in combination with endocrine therapies. A, Cells seeded in 96-well plates were treated with 1μM fulvestrant, 10μM riluzole (RIL), the combination, or DMSO control (vehicle, Veh) for 7 to 8 days prior to staining with crystal violet. Data are processed as the mean % growth for 5 or 6 technical replicates and represent 2 to 4 independent biological assays. The mean % growth data of a representative single technical replicate was then used to create a combination matrix used in SynergyFinder, and the results were presented as 2D surface plots. The SynergyFinder scores are shown at the top of the plots, highlighting the level of synergy. B and C, Graphical representation of the synergy scores from the riluzole/fulvestrant (B) and riluzole/4-hydroxytamoxifen (4HT) (C) combination using 3 models: Bliss, highest single agent (HSA), and zero interaction potency (ZIP).

Article Snippet: PDEs were treated with 100nM fulvestrant, 10μM riluzole, the combination, or solvent control (DMSO) for 48 hours before formalin fixation, paraffin embedding, sectioning, and staining for PCNA (1:1000, Santa Cruz Biotechnology Cat# sc-56, RRID:AB_628110), cleaved caspase 3 (1:300, Cell Signaling Technology Cat# 9661, RRID:AB_2341188), and Ki67 (1:500, Abcam Cat# ab16667, RRID:AB_302459).

Techniques: Control, Staining

Journal: Journal of the Endocrine Society

Article Title: Riluzole Suppresses Growth and Enhances Response to Endocrine Therapy in ER+ Breast Cancer

doi: 10.1210/jendso/bvad117

Figure Lengend Snippet: Riluzole plus fulvestrant significantly inhibits proliferation in primary breast tumor explant cultures. A, Pathologic data for 5 patient-derived explants (PDEs). ER, PR, and Ki67% are from the initial surgical specimen, and NOS = not otherwise specified. *denotes the PDE for which representative images are shown in panel C. B, PDEs were treated with 100nM fulvestrant, 10μM riluzole, the combination, or DMSO control (vehicle) for 2 days prior to formalin fixation, paraffin embedding, sectioning, and staining for PCNA by IHC. Data are presented as change relative to vehicle (set to 0) for each explant and analyzed by one-sample t test vs 0 (vehicle). * P = .013 Vehicle vs Combination. *denotes the PDE for which representative images are shown in panel C. C, Representative images of PCNA and Caspase-3 staining from PDE #1055 (ILC).

Article Snippet: PDEs were treated with 100nM fulvestrant, 10μM riluzole, the combination, or solvent control (DMSO) for 48 hours before formalin fixation, paraffin embedding, sectioning, and staining for PCNA (1:1000, Santa Cruz Biotechnology Cat# sc-56, RRID:AB_628110), cleaved caspase 3 (1:300, Cell Signaling Technology Cat# 9661, RRID:AB_2341188), and Ki67 (1:500, Abcam Cat# ab16667, RRID:AB_302459).

Techniques: Derivative Assay, Control, Staining