zr751 breast cancer cell lines  (ATCC)

Journal: Molecular Systems Biology

Article Title: Proteome-wide copy-number estimation from transcriptomics

doi: 10.1038/s44320-024-00064-3

Figure Lengend Snippet: ( A , B ) Knockdown of NUP37 increases CDK4 abundance in B2B1 breast epithelial cells (Wang et al, ). ( C , D ) Overexpression of inducible NUP37 (iNUP37) decreases CDK4 abundance in B2B1 breast epithelial cells. ( E , F ) Overexpression of iNUP37 decreases CDK4 abundance in MCF7 luminal breast cancer cells. ( G , H ) Residual DNM1L protein after knockdown correlates with CDK4 abundance in T47D ( G ) and ZR751 ( H ) luminal breast cancer cells. Actin was used as a housekeeping control not used for loading normalization (“Methods”). Quantities are scaled to shScramble control samples. Data information: For ( A , C , E ), representative immunoblots for NUP37 and CDK4 are shown with vinculin and tubulin ( A , C ) or p38 ( E ) as loading controls and FLAG ( C , E ) to confirm ectopic expression of iNUP37 or luciferase (luc) control. For ( B , D , F ), immunoblot results are summarized as the mean total NUP37 (endogenous ( B , D , F ) and induced ( D , F )) or CDK4 ± s.e.m. of n = 6 biological replicates. Differences were assessed by one-sided t test. For ( G , H ), representative immunoblots for DNM1L and CDK4 are shown with vinculin and p38 as loading controls and actin as a housekeeping control. Data are summaries from n = 6 biological replicates.

Article Snippet: ZR751 cells ( H. sapiens ) , ATCC , Cat # CRL-1500.

Techniques: Knockdown, Over Expression, Control, Western Blot, Expressing, Luciferase

Journal: Molecular Systems Biology

Article Title: Proteome-wide copy-number estimation from transcriptomics

doi: 10.1038/s44320-024-00064-3

Figure Lengend Snippet: Reagents and tools table

Article Snippet: ZR751 cells ( H. sapiens ) , ATCC , Cat # CRL-1500.

Techniques: Recombinant, Luciferase, Sequencing, Cloning, Software, Bicinchoninic Acid Protein Assay

Journal: The Journal of Cell Biology

Article Title: TLN1 contains a cancer-associated cassette exon that alters talin-1 mechanosensitivity

doi: 10.1083/jcb.202209010

Figure Lengend Snippet: TLN1 exon 17b inclusion is associated with altered drug response and gene dependencies in cancer cell lines. (A) Differential splicing of TLN1 exon 17b is detected in cancer cell lines. Boxplots show distribution of percent spliced-in (PSI) values for TLN1 exon 17b in lung, colon, and breast cancer cell lines. The individually labeled BT20, ZR751, MDA231, and BT549 breast cancer cell lines were used for RT-PCR validation in B. (B) RT-PCR validation of TLN1 exon 17b expression in four representative breast cancer cell lines. RT-PCR was performed with primers flanking exon 17b (primer positions indicated by black arrows). Exon 17b spans 51 base pairs (bp) and exon 17b inclusion results in an amplicon size increase from 183 bp to 234 bp. BT20 and ZR751 cell lines show exon 17b inclusion whereas MDA231 and BT549 cell lines show exon 17b skipping. (C) Expression of TLN1 inclusion junctions (18, 20) and skipping junction (19) was correlated to cell survival after drug treatment using DepMap drug sensitivity data across all cancer cell lines. The top-ranked correlation coefficients (FDR < 0.05 and |rho| > 0.2) were used to construct the SpliceRadar plot. TLN1 exon 17b inclusion (red and dark red lines) and exclusion (blue line) junction expression is plotted against their correlation coefficient with cell survival upon drug treatment. The data suggest that exon 17b inclusion is associated with increased sensitivity to EGFR inhibitors (blue boxes) and resistance to drugs targeting PI3K-Akt and cytoskeleton organization (red boxes). The black dashed line indicates a correlation coefficient R = 0 and an R range from −0.5 to 0.5 is shown. (D) KEGG gene set enrichment analysis (GSEA) of DepMap gene dependencies associated with TLN1 exon 17b inclusion in cancer cell lines. The enrichment plot shows the top over-represented pathways, including cell adhesion, cytoskeleton organization (red), and EGFR/ErbB signaling pathways (blue). Dot size represents the number of genes enriched in each KEGG pathway and the color gradient indicates significance level of adjusted P-values. (E) Combined TGF-β/EGF treatment promotes TLN1 exon 17b skipping in a SMAD3 and PCBP1-dependent manner. Gene-wise splice plots of TLN1 junction expression in HeLa cells, which show baseline inclusion of exon 17b. Left panel: Combined TGF-β/EGF treatment leads to exon 17b skipping in HeLa cells. Middle panel: shRNA-mediated knockdown of TGF-β signal transducer SMAD3 blocks the TGF-β/EGF-induced skipping of exon 17b in HeLa cells. Right panel: shRNA-mediated knockdown of the RNA-binding protein PCBP1 blocks the TGF-β/EGF-induced skipping of exon 17b in HeLa cells. (The plots shown in this figure were generated by DJExpress-based re-analysis of RNA-Seq data from GSE72419 ; gray area indicates the log-fold change cut-off (|logFC| > 0.5). Exon 17b inclusion junctions are shown in red, exon 17b skipping junction is shown in blue. Junctions with FDR > 0.05 for absolute or relative logFC (or both) are shown in black. Black arrow indicates the direction of TLN1 transcription on the reverse strand.

Article Snippet: BT20, BT549, MCF7, MCF10a, MDA-MB231, MDA-MB453, SKBR3, SUM44PE, T47D, and ZR751 cell lines were obtained from the American Type Culture Collection (ATCC), STR type verified by PCR, and cultured as described previously.

Techniques: Labeling, Reverse Transcription Polymerase Chain Reaction, Biomarker Discovery, Expressing, Amplification, Construct, Protein-Protein interactions, shRNA, Knockdown, RNA Binding Assay, Generated, RNA Sequencing

Journal: The Journal of Cell Biology

Article Title: TLN1 contains a cancer-associated cassette exon that alters talin-1 mechanosensitivity

doi: 10.1083/jcb.202209010

Figure Lengend Snippet: CLSTN1 exon 11 expression is inversely correlated with TLN1 exon 17b expression in cancer patients and cell lines. (A) Correlation analysis of percent spliced-in (PSI) values of TLN1 exon 17b and CLSTN1 exon 11 in tumor patient tissue and cancer cell lines. TLN1 exon 17b and CLSTN1 exon 11 splicing is inversely correlated, suggesting nearly trans-mutually exclusive splicing regulation of these two events ( R = Pearson correlation coefficient, P = adjusted P value). (B) RT-PCR validation of CLSTN1 exon 11 expression in four representative breast cancer cell lines. RT-PCR was performed with primers flanking exon 11 (primer positions indicated by black arrows). Exon 11 skipping results in an amplicon size reduction from 278 bp to 221 base pairs. BT20 and ZR751 cell lines show exon 11 skipping, whereas MDA231 and BT549 cell lines show exon 11 inclusion. The RT-PCR analysis of TLN1 exon 17b expression in cancer cell lines shown in was repurposed here to illustrate the inverse splicing pattern with CLSTN1 exon 11. (C) Analogous analysis to that reveals dynamic CLSTN1 exon 11 splicing in response to combined TGF-β/EGF treatment. Gene-wise splice plots of CLSTN1 junction expression in HeLa cells, which show baseline skipping of exon 11. The analysis of the TLN1 exon 17b expression in HeLa cells shown in was repurposed here to illustrate the inverse splicing pattern with CLSTN1 exon 11. (The plots shown in this figure were generated by DJExpress -based re-analysis of RNA-Seq data from GSE72419 ; gray area indicates the log-fold change cut-off (|logFC| > 0.5). Inclusion junctions are shown in red, skipping junctions are shown in blue. Junctions with FDR > 0.05 for absolute or relative logFC (or both) are shown in black. Black arrow indicates the direction of transcription on the reverse strand).

Article Snippet: BT20, BT549, MCF7, MCF10a, MDA-MB231, MDA-MB453, SKBR3, SUM44PE, T47D, and ZR751 cell lines were obtained from the American Type Culture Collection (ATCC), STR type verified by PCR, and cultured as described previously.

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Biomarker Discovery, Amplification, Generated, RNA Sequencing