breast cancer cell lines mcf7  (ATCC)

Journal: Science Advances

Article Title: Targeting SUV39H2 exon skipping reverses resistance to CDK4/6 inhibitors via transcriptional activation of p21

doi: 10.1126/sciadv.aea2001

Figure Lengend Snippet: ( A ) Pie plots depicting the proportion of types of the differential AS events between EndoR (endocrine resistant) and EndoR/PalR (endocrine therapy/palbociclib resistant) cells. ES: exon skipping, IR: intron retention, MXE: mutually exclusive exon, A5SS: alternative 5′ splice sites, A3SS: alternative 3′ splice sites. ( B ) Volcano plots of the differential ES events between EndoR and EndoR/PalR cells established from MCF7 and T47D cells ( GSE150997 ). ( C ) Distribution of the differential ES events between EndoR and EndoR/PalR cells on regions of protein-coding genes. ( D ) Venn diagrams showing the overlapping differential ES events between EndoR and EndoR/PalR cells from MCF7 and T47D cells. ( E ) GO analysis of the overlapping differential ES events. Heatmaps showing the significantly enriched differential ES events from high to low ΔPSI. GRN_1 and GRN_2 refer to 2 ES events in GRN . ( F ) A sashimi plot of ES in SUV39H2 exon 2 of EndoR and EndoR/PalR cells. ( G ) RT-PCR detection of SUV39H2 exon 2 in MCF7-TAMR, MCF7-PALR, and MCF7-ABER cells. ( H ) A scheme showing SUV39H2 exon 2 skipping introduces a PTC, which leads to products with no enzymatic activity and may undergo NMD. SET: Su(var)3-9, Enhancer-of-zeste, Trithorax domain; Chromo: Chromodomain. ( I ) SUV39H2 mRNA levels were detected in MCF7-TAMR, MCF7-PALR, and MCF7-ABER cells treated with actinomycin D ( N = 3 biological replicates). ( J and K ) Detection of SUV39H2 mRNA (J) and protein (K) levels in MCF7-TAMR, MCF7-PALR, and MCF7-ABER cells. In (G), (I), (J), and (K), data are shown as means ± SD ( N = 3 biological replicates). The P values were calculated by a two-tailed unpaired Student’s t test for two-group comparison and one-way analysis of variance (ANOVA) followed by Tukey’s test for multiple-group comparison. h, hours.

Article Snippet: Breast cancer cell lines MCF7 [American Type Culture Collection (ATCC) HTB-22], T47D (ATCC, HTB-133), ZR-75-1 (ATCC, CRL-1500), SUM159 (Procell, CL-0622), MDA-MB-231 (ATCC, CRM-HTB-26), MDA-MB-468 (Procell, CL-0290), and the immortalized breast epithelium cell MCF10A (ATCC, CRL-10317) were STR validated (Shanghai Biowing Applied Biotechnology Co.) and screened for mycoplasma contamination using MycoBlue Mycoplasma Detector (Vazyme, D101-01).

Techniques: Analysis, Reverse Transcription Polymerase Chain Reaction, Activity Assay, Two Tailed Test, Comparison

Journal: Science Advances

Article Title: Targeting SUV39H2 exon skipping reverses resistance to CDK4/6 inhibitors via transcriptional activation of p21

doi: 10.1126/sciadv.aea2001

Figure Lengend Snippet: ( A ) Schematic representation of microwalk ASOs designed targeting SUV39H2 exon 2. ( B ) RT-PCR detection of SUV39H2 exon 2 in MCF7-ABER transfected with Ctr-ASO or SUV-ASOs ( N = 3 biological replicates). ( C ) RT-qPCR detection of SUV39H2 mRNA levels in MCF7 and MCF7-ABER transfected with Ctr-ASO or SUV-ASOs. ( D ) Western blotting detection of SUV39H2 and H3K9me3 protein levels in MCF7 and MCF7-ABER transfected with Ctr-ASO or SUV-ASOs. ( E ) RT-PCR detection of SUV39H2 exon 2 in MCF7 and MCF7-ABER transfected with increasing concentrations of SUV-ASO2 ( N = 3 biological replicates), and the EC 50 was calculated. ( F ) Schematic representation of further modified ASO (ASO-M) designed targeting SUV39H2 exon 2. AS, alternative splicing. ( G ) The secondary structure of SUV39H2 mRNA was predicted by RNAFold. ( H ) The docking of SUV39H2 mRNA and SUV-ASO2-M was performed with AlphaFold3, and PDBePISA calculated the ΔG. ( I ) RT-PCR detection of SUV39H2 exon 2 in MCF7 and MCF7-ABER was treated with an increasing concentration of SUV-ASO2-M ( N = 3 biological replicates), and the EC 50 was calculated. ( J ) RT-qPCR detection of SUV39H2 mRNA levels in MCF7 and MCF7-ABER treated with Ctr-ASO-M or SUV-ASO2-M. ( K ) Western blotting detection of SUV39H2 protein levels in MCF7 and MCF7-ABER treated with Ctr-ASO-M or SUV-ASO2-M. In (B), (C), (D), (E), (I), (J), and (K), data were presented as means ± SD ( N = 3 biological replicates). The P values were calculated by a two-tailed unpaired Student’s t test for two-group comparison and one-way ANOVA followed by Tukey’s test for multiple-group comparison.

Article Snippet: Breast cancer cell lines MCF7 [American Type Culture Collection (ATCC) HTB-22], T47D (ATCC, HTB-133), ZR-75-1 (ATCC, CRL-1500), SUM159 (Procell, CL-0622), MDA-MB-231 (ATCC, CRM-HTB-26), MDA-MB-468 (Procell, CL-0290), and the immortalized breast epithelium cell MCF10A (ATCC, CRL-10317) were STR validated (Shanghai Biowing Applied Biotechnology Co.) and screened for mycoplasma contamination using MycoBlue Mycoplasma Detector (Vazyme, D101-01).

Techniques: Reverse Transcription Polymerase Chain Reaction, Transfection, Quantitative RT-PCR, Western Blot, Modification, Alternative Splicing, Docking Assay, Concentration Assay, Two Tailed Test, Comparison

Journal: Science Advances

Article Title: Targeting SUV39H2 exon skipping reverses resistance to CDK4/6 inhibitors via transcriptional activation of p21

doi: 10.1126/sciadv.aea2001

Figure Lengend Snippet: ( A ) MCF7-PALR and MCF7-ABER cells were treated with Ctr-ASO-M or SUV-ASO-Ms (0.1 μM). CCK8 assays reveal the cell growth under PAL (0.5 μM) or ABE (0.1 μM) treatment ( N = 3 biological replicates). ( B ) CCK8 assays calculating IC 50 values of SUV-ASO-Ms in MCF7-TAMR, MCF7-PALR, and MCF7-ABER cells ( N = 3 biological replicates). ( C ) Synergy Finder is calculating ZIP scores in MCF7-TAMR to study the synergistic effect between SUV-ASO-Ms and CDK4/6i (PAL and ABE). ( D and E ) MCF7-PALR and MCF7-ABER cells were treated with Ctr-ASO-M or SUV-ASO-Ms (0.1 μM) alone or in combination with CDK4/6i (PAL, 0.5 μM and ABE, 0.1 μM). Flow cytometry analysis (D) and β-Gal activity assays (20× magnification) (E) showing the cell cycle distribution and senescence of the cells. ( F ) Schematic depicting the experimental design of the MCF7-ABER xenograft tumors conducted to assess the efficacy of SUV-ASO2-M or a combination of SUV-ASO2-M with ABE in vivo. ( G to I ) After being treated with Ctr-ASO-M or SUV-ASO2-M in combination with Veh or ABE, the tumor growth curves (G), the harvested tumors (H), and the tumor weight (I) were measured. ( J and K ) RT-qPCR and Western blotting detection of SUV39H2 mRNA (J) and protein (K) in tumors from xenografts. ( L ) IHC staining of p21 in tumors from xenografts. H scores were calculated for p21 in all samples. Data were presented as means ± SD [(A to E), N = 3 biological replicates; (G), (I), (J) to (L), N = 5 biological replicates]. The P values were calculated by one-way ANOVA followed by Tukey’s test for multiple-group comparison.

Article Snippet: Breast cancer cell lines MCF7 [American Type Culture Collection (ATCC) HTB-22], T47D (ATCC, HTB-133), ZR-75-1 (ATCC, CRL-1500), SUM159 (Procell, CL-0622), MDA-MB-231 (ATCC, CRM-HTB-26), MDA-MB-468 (Procell, CL-0290), and the immortalized breast epithelium cell MCF10A (ATCC, CRL-10317) were STR validated (Shanghai Biowing Applied Biotechnology Co.) and screened for mycoplasma contamination using MycoBlue Mycoplasma Detector (Vazyme, D101-01).

Techniques: Flow Cytometry, Analysis, Activity Assay, Xenograft Assay, In Vivo, Quantitative RT-PCR, Western Blot, Immunohistochemistry, Comparison

Journal: Science Advances

Article Title: Targeting SUV39H2 exon skipping reverses resistance to CDK4/6 inhibitors via transcriptional activation of p21

doi: 10.1126/sciadv.aea2001

Figure Lengend Snippet: ( A ) GSEA comparison of patients with breast cancer with high ( n = 100) or low ( n = 100) PSI values of SUV39H2 exon 2 (TCGA-BRCA dataset). ( B ) Volcano plots of RNA-seq data of MCF7-PALR and MCF7-ABER cells treated with Ctr-ASO or SUV-ASO2-M (0.1 μM) showing numerous DEGs upon SUV-ASO2-M treatment. ( C ) GSEA comparison of MCF7-PALR and MCF7-ABER cells treated with Ctr-ASO or SUV-ASO2-M. ( D ) REACTOME analysis of top 100 up-regulated genes (SUV-ASO2-M versus Ctr-ASO) in MCF7-ABER cells. ( E and F ) RT-qPCR (E) and Western blotting (F) validation of up-regulated genes (SUV-ASO2-M versus Ctr-ASO-M) in MCF7-PALR and MCF7-ABER cells from RNA-seq data. In (E) and (F), data were presented as means ± SD ( N = 3 biological replicates). The P values were calculated by one-way ANOVA followed by Tukey’s test for multiple-group comparison.

Article Snippet: Breast cancer cell lines MCF7 [American Type Culture Collection (ATCC) HTB-22], T47D (ATCC, HTB-133), ZR-75-1 (ATCC, CRL-1500), SUM159 (Procell, CL-0622), MDA-MB-231 (ATCC, CRM-HTB-26), MDA-MB-468 (Procell, CL-0290), and the immortalized breast epithelium cell MCF10A (ATCC, CRL-10317) were STR validated (Shanghai Biowing Applied Biotechnology Co.) and screened for mycoplasma contamination using MycoBlue Mycoplasma Detector (Vazyme, D101-01).

Techniques: Comparison, RNA Sequencing, Analysis, Quantitative RT-PCR, Western Blot, Biomarker Discovery

Journal: Science Advances

Article Title: Targeting SUV39H2 exon skipping reverses resistance to CDK4/6 inhibitors via transcriptional activation of p21

doi: 10.1126/sciadv.aea2001

Figure Lengend Snippet: ( A ) Average distribution of ATAC-seq signal around promoters (±3 kb from TSS) and enhancers in MCF7-ABER cells treated with Ctr-ASO-M or SUV-ASO2-M (0.1 μM). ( B ) A volcano plot comparing Footprint TF activity between MCF7-ABER cells treated with Ctr-ASO-M or SUV-ASO2-M. ( C ) Footprint TF activity of NFYA between MCF7-ABER cells treated with Ctr-ASO-M or SUV-ASO2-M. ( D ) A volcano plot of DAPs between MCF7-ABER cells treated with Ctr-ASO-M and SUV-ASO2-M. ( E ) Category of DAPs according to their status (open or closed) and location (proximal or distal from TSS) in the genome. ( F ) Overlapping of up-regulated DEGs and open DAPs in MCF7-ABER cells treated with SUV-ASO2-M. The overlapped genes were analyzed using KEGG enrichment. ( G ) A heatmap of the overlapped genes enriched in the p53 pathway, senescence, or both processes. ( H ) IGV visualization of DAPs in p21 , GADD45A , and SERPINE1 of MCF7-ABER cells treated with Ctr-ASO-M or SUV-ASO2-M.

Article Snippet: Breast cancer cell lines MCF7 [American Type Culture Collection (ATCC) HTB-22], T47D (ATCC, HTB-133), ZR-75-1 (ATCC, CRL-1500), SUM159 (Procell, CL-0622), MDA-MB-231 (ATCC, CRM-HTB-26), MDA-MB-468 (Procell, CL-0290), and the immortalized breast epithelium cell MCF10A (ATCC, CRL-10317) were STR validated (Shanghai Biowing Applied Biotechnology Co.) and screened for mycoplasma contamination using MycoBlue Mycoplasma Detector (Vazyme, D101-01).

Techniques: Activity Assay

Journal: Science Advances

Article Title: Targeting SUV39H2 exon skipping reverses resistance to CDK4/6 inhibitors via transcriptional activation of p21

doi: 10.1126/sciadv.aea2001

Figure Lengend Snippet: ( A ) H3K9me3 signals (CUT&Tag) around promoters and enhancers in MCF7-ABER cells treated with Ctr-ASO-M or SUV-ASO2-M (0.1 μM). ( B ) RAD21 signals (ChIP-seq) around enhancers in MCF7 cells ( GSE25021 and GSE72082 datasets). ( C ) RAD21 signals (ChIP-seq) around SUV39H2-dependent and independent H3K9me3 peaks. ( D ) A volcano plot of DEGs between the RAD21 overexpression and the control group (MCF7-ABER). ( E ) GSEA of transcriptome between RAD21 overexpression and the control. ( F and G ) Western blotting (F) and RT-qPCR (G) detection of RAD21 and p21 protein levels, and p21 mRNA levels in MCF7-PALR and MCF7-ABER cells with RAD21 overexpression. ( H ) IGV visualization of H3K9me3, RAD21, STAG1, and SMC1A signals in the p21 promoter ( p21 -Pro) and distal enhancer ( p21 -SE). Blue box: cohesin binding site; gray box: differential H3K9me3 peak. ( I and J ) ChIP-qPCR of H3K9me3 (I) and RAD21 (J) in p21 -Pro and p21 -SE of MCF7-PALR and MCF7-ABER cells treated with Ctr-ASO-M or SUV-ASO2-M (0.1 μM). ( K ) ChIP-qPCR of SUV39H2 in p21 -Pro and p21 -SE of MCF7-PALR and MCF7-ABER cells. ( L ) Western blotting of RAD21, SUV39H2, and p21 protein levels in MCF7-ABER cells transfected with Ctr siRNA or RAD21 siRNA and then treated with Ctr-ASO-M or SUV-ASO2-M (0.1 μM). ( M ) MCF7-ABER cells were transfected with Ctr siRNA or RAD21 siRNA1. CCK8 assays showing cell growth in cells treated with Ctr-ASO-M or SUV-ASO2-M (0.1 μM) in combination with ABE (0.1 μM). ( N ) MCF7-ABER cells were transfected with Ctr siRNA or RAD21 siRNA1. β-Gal activity assays (20× magnification) revealing the senescent cells treated with Ctr-ASO-M or SUV-ASO2-M (0.1 μM). In (F), (G), (I) to (N), data were presented as means ± SD ( N = 3 biological replicates). The P values were calculated using a two-tailed unpaired Student’s t test for two-group comparison and one-way ANOVA followed by Tukey’s test for multiple-group comparisons.

Article Snippet: Breast cancer cell lines MCF7 [American Type Culture Collection (ATCC) HTB-22], T47D (ATCC, HTB-133), ZR-75-1 (ATCC, CRL-1500), SUM159 (Procell, CL-0622), MDA-MB-231 (ATCC, CRM-HTB-26), MDA-MB-468 (Procell, CL-0290), and the immortalized breast epithelium cell MCF10A (ATCC, CRL-10317) were STR validated (Shanghai Biowing Applied Biotechnology Co.) and screened for mycoplasma contamination using MycoBlue Mycoplasma Detector (Vazyme, D101-01).

Techniques: ChIP-sequencing, Over Expression, Control, Western Blot, Quantitative RT-PCR, Binding Assay, ChIP-qPCR, Transfection, Activity Assay, Two Tailed Test, Comparison

Journal: Science Advances

Article Title: Targeting SUV39H2 exon skipping reverses resistance to CDK4/6 inhibitors via transcriptional activation of p21

doi: 10.1126/sciadv.aea2001

Figure Lengend Snippet: ( A ) Volcano plots of the differentially expressed RBPs between EndoR and EndoR/PalR cells established from MCF7 and T47D cells ( GSE150997 ). ( B ) Overlapping of down-regulated RBPs between EndoR and EndoR/PalR cells established from MCF7 and T47D cells ( GSE150997 ). ( C ) Western blotting detection of ESRP1 and SUV39H2 protein levels in MCF7 and T47D cells transfected with Ctr siRNA or ESRP1 siRNA. ( D ) Western blotting detection of ESRP1 protein levels in MCF7-TAMR, MCF7-PALR, and MCF7-ABER cells. ( E and F ) RT-qPCR detection of SUV39H2 mRNA levels (E) and RT-PCR detection of SUV39H2 exon 2 (F) in MCF7 and T47D cells transfected with Ctr siRNA or ESRP1 siRNA. ( G ) Conservation analysis of the putative ESRP1-binding site in SUV39H2 exon 2. ( H ) Minigene assays of MCF7-ABER cells transfected with Ctr siRNA or ESRP1 siRNA in combination with pSPL3-SUV-W or pSPL3-SUV-M. RT-PCR was performed to detect SUV39H2 exon 2 in each group. ( I ) RIP-qPCR detection of ESRP1 binding to SUV39H2 mRNA in MCF7 and T47D cells. ( J ) Model illustrating the antitumor function of SUV-ASO2-M in CDK4/6i-resistant breast cancer cells. Free-uptake of SUV-ASO2-M promotes RNase H–dependent degradation of SUV39H2 RNA and skipping of SUV39H2 exon 2, resulting in decreased SUV39H2 protein expression in CDK4/6i-resistant breast cancer cells. Consequently, the H3K9me3 mark near the p21 distal enhancer is removed, followed by binding of the cohesin complex and interaction between the distal enhancer and the promoter of p21 . Next, the chromatin accessibility of the p21 promoter is increased to drive transcriptional activation of p21 . In (C) to (F) and (H) to (I), data were presented as means ± SD ( N = 3 biological replicates). The P values were calculated by a two-tailed unpaired Student’s t test for two-group comparison and one-way ANOVA followed by Tukey’s test for multiple-group comparisons.

Article Snippet: Breast cancer cell lines MCF7 [American Type Culture Collection (ATCC) HTB-22], T47D (ATCC, HTB-133), ZR-75-1 (ATCC, CRL-1500), SUM159 (Procell, CL-0622), MDA-MB-231 (ATCC, CRM-HTB-26), MDA-MB-468 (Procell, CL-0290), and the immortalized breast epithelium cell MCF10A (ATCC, CRL-10317) were STR validated (Shanghai Biowing Applied Biotechnology Co.) and screened for mycoplasma contamination using MycoBlue Mycoplasma Detector (Vazyme, D101-01).

Techniques: Western Blot, Transfection, Quantitative RT-PCR, Reverse Transcription Polymerase Chain Reaction, Analysis, Binding Assay, Expressing, Activation Assay, Two Tailed Test, Comparison

Journal: Chemical Biology & Drug Design

Article Title: Triazole‐Linked Pyrimidine Nucleoside Dimers: Design, Synthesis, and Applications in Medicinal and Nucleic Acid Chemistry. Part IV

doi: 10.1111/cbdd.70407

Figure Lengend Snippet: In vitro cytotoxic activity (IC 50 , μM).

Article Snippet: GBM cell lines (U‐251 MG, U‐138 MG), SK‐OV‐3 (ovarian cancer cell line), HeLa (cervical cancer cell line), T47D (breast cancer cell line), and non‐cancerous lung fibroblast cell line (MRC‐5) were purchased from ATCC (Manassas, USA).

Techniques: In Vitro, Activity Assay

Journal: Advanced Science

Article Title: Self‐Assembling Peptide‐Adjuvant Conjugate (SaPAC) Platform for Precision Cancer Immunotherapy

doi: 10.1002/advs.77632

Figure Lengend Snippet: Synergistic antitumor efficacy of trivalent SaPAC‐4T1 vaccination combined with anti‐PD‐1 checkpoint blockade in orthotopic 4T1 TNBC. (A) Treatment timeline. (B) Representative endpoint tumors (day 16; scale bar, 10 mm). (C) Longitudinal tumor volumes ( n = 6–8 mice/group). (D) Terminal tumor volumes on day 15. (E,F) Individual tumor growth trajectories. Data are the mean ± SEM; significance was assessed by unpaired two‐tailed Student's t‐test ( * p <0.05, ** p <0.01, *** p <0.001 vs. mock + anti‐PD‐1).

Article Snippet: The DC2.4 cell line, mouse bladder cancer cell line MB49, mouse melanoma cell line B16F10, and the mouse breast cancer cell line 4T1 were purchased from ATCC.

Techniques: Two Tailed Test

Journal: Advanced Science

Article Title: Self‐Assembling Peptide‐Adjuvant Conjugate (SaPAC) Platform for Precision Cancer Immunotherapy

doi: 10.1002/advs.77632

Figure Lengend Snippet: Peptides, peptide‐adjuvant conjugates, and fluorescently labeled peptides used in this study. The antigen epitope, linker/self‐assembly residues, and 1V209‐conjugated lysines (K * ) are indicated in the sequence column.

Article Snippet: The DC2.4 cell line, mouse bladder cancer cell line MB49, mouse melanoma cell line B16F10, and the mouse breast cancer cell line 4T1 were purchased from ATCC.

Techniques: Labeling, Sequencing, Conjugation Assay

Journal: Cancer Discovery

Article Title: Senescent-Like Neutrophils Shape Angiogenic Immunosuppressive Niches in Colorectal Cancer Liver Metastasis

doi: 10.1158/2159-8290.CD-25-0820

Figure Lengend Snippet: Tissue specification of neutrophils in the CRLM microenvironment. A, Expression levels of CXCR4, CXCR2, and CXCR1 across each TAN and PMN subset. B, mIHC staining of MPO, CXCR1, CXCR2, and CXCR4 in colorectal cancer and CRLM tissues. Scale bar, 50µm. C, Quantitative analysis of the percentage of CXCR1 + , CXCR2 + , and CXCR4 + neutrophils in paired colorectal cancer and CRLM tissues ( n = 5). D, Heatmap showing the mean strength of chemokine–receptor axis for each TAN subset in CRLM tissues. E, Predicted ordering of each TAN subset by CytoTRACE analysis using scRNA-seq dataset. F, Monocle 2 trajectory analysis of TAN subsets differentiation using the scRNA-seq dataset. Cells are colored by pseudotime, ordering predicted by CytoTRACE, and cell types. G, The density of each TAN subset along pseudotime. H, Clustering analysis of gene expression along pseudotime, with pathway enrichment analysis of four gene sets based on pseudotime. I, TAN1 similarity scores of TAN0_ELL2, TAN2_HSPA1B, TAN3_IFIT2, and TAN4_ARG1 across colorectal cancer, adjacent liver tissues (LP), and CRLM tissues. The TAN1 similarity score was calculated based on the top 50 differentially expressed genes in TAN1. J, Relative mRNA expression levels of BHLHE40 , CDKN1A (p21), LGALS3 , VEGFA , and LDHA as determined by qPCR in control neutrophils or neutrophils cocultured with HCT116 or DLD-1 cells. K and L, Flow cytometry analysis of Gal3 surface expression in neutrophils cultured alone (control) or cocultured with DLD-1 ( K ) or HCT116 cells ( L ). P values were determined by paired Student t test ( C ) or unpaired Student t test ( J , K , and L ). n.s., not significant; **, P < 0.01; ***, P < 0.001. CRC, colorectal cancer; Ctrl, control; MFI, mean fluorescence intensity.

Article Snippet: The human colon cancer cell lines HCT116 (RRID: CVCL_0291) and DLD-1 (RRID: CVCL_0248), mouse colon cancer cell line CT26 (RRID: CVCL_7254), as well as the human neutrophil cell line HL-60 (RRID: CVCL_0002) were obtained from the American Type Culture Collection.

Techniques: Tissue, Expressing, Staining, Analysis, Gene Expression, Control, Flow Cytometry, Cell Culture, Fluorescence