Journal: Nature Communications

Article Title: Unbiased discovery of cancer pathways and therapeutics using Pathway Ensemble Tool and Benchmark

doi: 10.1038/s41467-024-51859-9

Figure Lengend Snippet: a Plots showing the survival rate, measured by CCK-8 assay, of cervical (Hela) and bladder (T24 and UMUC3) cancer cell lines treated with different concentration of vehicle or indicated drugs for 72 h. The selective targets of CDK inhibitors are shown in parenthesis. Mean +/− sem from n > 3 biological replicates. b Plot showing expression of the CDK9 gene versus the unfavorability score for each bladder cancer cell line in the CCLE database . The color scale represents the IC50 values reported by the GDSC database for the CDK9-specific inhibitor CDK9_5038. Cell lines for which IC50 values are not available are highlighted in gray. The Spearman correlation value and corresponding p -value are shown in red. The center line and error bars indicate the trend line and 95% confidence interval. Selected cell lines are labeled. c Heatmap showing differentially expressed genes (DEGs; 3-fold at adjusted p -value < 0.05) between DMSO or CCT068127 (1uM) treated T24 cells for 48 h in n = 3 independent biological replicates. GSEA plots showing enrichment of genes repressed by the CDK4/6 inhibitor Palbociclib (top) or genes repressed by the CDK9 inhibitor VIP152 (bottom) in T24 cells treated 48 h with the CDK2/9 inhibitor CCT068127 (1 uM) or DMSO control. Palbociclib (SRP404373) or VIP152 inhibited genes are publicly sourced. d GSEA plot showing enrichment of transcriptomes of CCT068127 (1 uM) or DMSO treated T24 cells in favorable (top) or unfavorable (bottom) PET identified prognosis genes in bladder cancer. Shown are the FDR value and normalized enrichment score (NES). e Schematic of xenograft experiment and treatment plan with 30 mg/kg daily i.p. injections of CCT068127 or DMSO carrier. p -values compare DMSO-treated to CCT068127-treated groups at each time-point. f Plot showing daily tumor volumes during course of experiment. g Bar plots showing the mass of tumors at explant on day 23. Error bars show mean ± s.d. p -values in a and f are by two-way ANOVA with multiple comparisons adjustment and in g by two-sided Wilcoxon rank sum test. ns non-significant; * p < 0.01; ** p < 0.001; *** p < 0.0001. Panel e Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license ( https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en ). Source data are provided as a Source Data file.

Article Snippet: T-24 and UMUC3, human urinary bladder cancer cells were acquired from ATCC (HTB-4 TM and CRL-1749 TM , respectively).

Techniques: CCK-8 Assay, Concentration Assay, Expressing, Labeling, Control

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Long noncoding RNA MALAT1 is dynamically regulated in leader cells during collective cancer invasion.

doi: 10.1073/pnas.2305410120

Figure Lengend Snippet: Fig. 1. A dual double-stranded LNA nanobiosensor for probing lncRNA dynamics during collective cancer invasion. (A), Schematics of the FRET-based LNA nanobiosensor for detecting lncRNA in leader and follower cells. (B), Intracellular distributions of β-actin, MALAT1, and UCA1 RNA expressions detected by the nanobiosensors in live cancer cells (5,637). (Scale bars, 10 µm.) Images are representative of eight experiments. (C), Time-lapse images for MALAT1 dynamics in leader cells (marked by white arrows) during collective cell migration. (Scale bars, 30 µm.) Images are representative of five experiments. (D), Detection of MALAT1 expression in 3D tumor spheroids derived from patients with muscle-invasive bladder cancer. Blue dashed squares indicate the zoom-in regions (Right). Black arrows indicate protruding structures with leader cells sprouting from the spheroids. [Scale bars, 200 µm (Left) and 40 µm (Right).] Images are representative of six (Stage II) and ten (Stage IIIB) tumor spheroids. (E), 3D rendering of a cancer spheroid with leader cells (white arrows) and dissociated cancer cells (white arrowheads). (Scale bar, 200 µm.)

Article Snippet: The human bladder cancer cell line 5,637 from American Type Culture Collection (Manassas, VA) was cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 10 mg/mL Gentamicin (Fisher Scientific, Hampton, NH).

Techniques: Migration, Expressing, Derivative Assay

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Long noncoding RNA MALAT1 is dynamically regulated in leader cells during collective cancer invasion.

doi: 10.1073/pnas.2305410120

Figure Lengend Snippet: Fig. 2. LNA nanobiosensors detect TGF-β-induced MALAT1 upregulation in cell nuclei and cytoplasm. (A–C), Confocal images of β-actin mRNA, MALAT1, and UCA1 in live bladder cancer cells (5,637). The cells were treated with buffer control and TGF-β. FRET channels (Left), merged FRET and brightfield channels (Middle), and zoom-in views of single cells (Right) are shown to illustrate the expression distributions. Images are representative of five experiments. [Scale bars, 50 μm (Left and Middle), 10 μm (Right).] (D and E), Relative expression of β-actin, MALAT1, and UCA1 RNA (D) in whole cells and (E) colocalized with the nuclei. One-way ANOVA followed by Tukey’s post hoc test was used to compare transcript numbers between control and TGF-β treatment (n = 5, NS not significant, *P < 0.05, ****P < 0.0001).

Article Snippet: The human bladder cancer cell line 5,637 from American Type Culture Collection (Manassas, VA) was cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 10 mg/mL Gentamicin (Fisher Scientific, Hampton, NH).

Techniques: Control, Expressing

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Long noncoding RNA MALAT1 is dynamically regulated in leader cells during collective cancer invasion.

doi: 10.1073/pnas.2305410120

Figure Lengend Snippet: Fig. 5. MALAT1 expression is associated with the clinical stage of bladder cancer patient-derived cancer cells. (A), β-actin mRNA and MALAT1 expressions in cancer cells derived from bladder cancer patients. (Scale bars, 300 µm.) (B and C), MALAT1 is up-regulated in the stage IIIB sample compared to the stage II sample. (D), The portion of cells with a high level of MALAT1. Student’s t test was used to compare between samples (n ≥ 1,148 for gene expression and n = 5 for cell portions with an enhanced MALAT1 expression).

Article Snippet: The human bladder cancer cell line 5,637 from American Type Culture Collection (Manassas, VA) was cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 10 mg/mL Gentamicin (Fisher Scientific, Hampton, NH).

Techniques: Expressing, Derivative Assay, Gene Expression

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Long noncoding RNA MALAT1 is dynamically regulated in leader cells during collective cancer invasion.

doi: 10.1073/pnas.2305410120

Figure Lengend Snippet: Fig. 6. MALAT1 is associated with leader cells in tumor spheroids derived from muscle-invasive bladder cancer patients. (A–G), MALAT1 expression in 3D human tumor spheroids derived from bladder cancer patients. Clinical samples of stage II (DT2101 and DT2334), Stage IIIA (DT2092 and DT2148), Stage III (DT2153 and DT2115), and Stage IV (DT2296) were included to cover the spectrum of muscle-invasive bladder cancer. Blue dashed squares highlight the zoom-in views (Bottom) with leader cells (black arrows) or dissociated cells (black arrowheads). [Scale bars, 200 µm (Top) and 100 µm (Bottom).] Images are representative of at least six spheroids. (H and I), The number of detached cells and protrusions per spheroid on day 3 (n = 5). (J–L), Correlation of the spheroid volume, the number of detached cells, and the number of leader cells with MALAT1 expression on day 3. At least five spheroids were analyzed for each sample, and all detectable leader cells and detached cells were analyzed.

Article Snippet: The human bladder cancer cell line 5,637 from American Type Culture Collection (Manassas, VA) was cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 10 mg/mL Gentamicin (Fisher Scientific, Hampton, NH).

Techniques: Derivative Assay, Expressing