Journal: International Journal of Molecular Sciences

Article Title: Extracellular Acidosis Differentially Regulates Estrogen Receptor β-Dependent EMT Reprogramming in Female and Male Melanoma Cells

doi: 10.3390/ijms232315374

Figure Lengend Snippet: EMT in ERβ silenced melanoma cell lines. mRNA level of ERβ, N-cadherin, and vimentin in WM266-4 ( A ), M21 ( B ) female melanoma cells and in HS294t ( C ) and SKMEL2 ( D ) male melanoma cells. ( E ) Invasive ability of male and female melanoma cells silenced for ERβ, grown in standard pH or acidic pH medium. Invasiveness was performed using Matrigel-coated filters and it was measured as a percentage of the control. Data are expressed as means ± SEM of three independent experiments. * p < 0.05.

Article Snippet: Experiments were performed also using some of the most commonly used human melanoma cell lines of both sexes: WM266-4 (obtained from American Type Culture Collection (ATCC), Manassas, VA) and M21 (kindly provided by Dr. Antony Montgomery, The Scripps Research Institute, La Jolla, CA, USA), derived from female patients; HS294t and SkMel2 (obtained from ATCC), derived from male patients.

Techniques: Control

Journal: International Journal of Molecular Sciences

Article Title: Development of Sesamol Carbamate-L-Phenylalanine Prodrug Targeting L-Type Amino Acid Transporter1 (LAT1) as a Potential Antiproliferative Agent against Melanoma

doi: 10.3390/ijms23158446

Figure Lengend Snippet: Cellular uptake of sesamol (◇), sesamol prodrug ( ☐ ), and sesamol prodrug co-incubated with 1 mM BCH ( ○ ) in melanoma SK-MEL-2 cells. The uptake rates were fitted with a nonlinear least-squares kinetics model and are represented as dash line ( -- ), dot line ( ··· ), and straight line (−) for prodrug, prodrug with 1 mM BCH, and sesamol uptakes, respectively. Data are expressed as mean ± standard deviation of three replicates.

Article Snippet: Human LAT1 (SLC7A5) transfected in Flp-In™-293 human embryonic kidney (HEK293) cells (R750-07, Invitrogen, CA, USA), African green monkey kidney epithelial Vero cell (ATCC#CCL-81), and human melanoma SK-MEL-2 cells (CLS-Cell lines Service, Eppelheim, Germany) were maintained in DMEM with 10% FBS, 100 unit/mL of penicillin, and 100 µg/mL of streptomycin at 37 °C in 5% CO 2 atmosphere.

Techniques: Incubation, Standard Deviation

Journal: International Journal of Molecular Sciences

Article Title: Development of Sesamol Carbamate-L-Phenylalanine Prodrug Targeting L-Type Amino Acid Transporter1 (LAT1) as a Potential Antiproliferative Agent against Melanoma

doi: 10.3390/ijms23158446

Figure Lengend Snippet: In vitro stability testing of sesamol prodrug ( ☐ ) and its parent compound—sesamol (◇). An amount of 10 µM of sesamol prodrug dissolved in ( A ) SK-MEL-2 lysate in PBS pH 7.4 compared with 10 µM of sesamol prodrug dissolved in ( B ) PBS pH 7.4. Standard deviations were low: error bars smaller than the symbols.

Article Snippet: Human LAT1 (SLC7A5) transfected in Flp-In™-293 human embryonic kidney (HEK293) cells (R750-07, Invitrogen, CA, USA), African green monkey kidney epithelial Vero cell (ATCC#CCL-81), and human melanoma SK-MEL-2 cells (CLS-Cell lines Service, Eppelheim, Germany) were maintained in DMEM with 10% FBS, 100 unit/mL of penicillin, and 100 µg/mL of streptomycin at 37 °C in 5% CO 2 atmosphere.

Techniques: In Vitro

Journal: International Journal of Molecular Sciences

Article Title: Development of Sesamol Carbamate-L-Phenylalanine Prodrug Targeting L-Type Amino Acid Transporter1 (LAT1) as a Potential Antiproliferative Agent against Melanoma

doi: 10.3390/ijms23158446

Figure Lengend Snippet: Cytotoxicity of ( A ) sesamol prodrug and ( B ) sesamol in SK-MEL-2 cells at various times. ( C ) Cytotoxicity of sesamol prodrug compared with sesamol prodrug with 1 mM BCH in SK-MEL-2 cells. ( D ) Cytotoxicity of sesamol prodrug compared with sesamol at 96 h in Vero cells. Data are expressed as means ± standard deviations of three replicates. A p -value less than 0.05 is statistically significant.

Article Snippet: Human LAT1 (SLC7A5) transfected in Flp-In™-293 human embryonic kidney (HEK293) cells (R750-07, Invitrogen, CA, USA), African green monkey kidney epithelial Vero cell (ATCC#CCL-81), and human melanoma SK-MEL-2 cells (CLS-Cell lines Service, Eppelheim, Germany) were maintained in DMEM with 10% FBS, 100 unit/mL of penicillin, and 100 µg/mL of streptomycin at 37 °C in 5% CO 2 atmosphere.

Techniques:

Journal: Nature Communications

Article Title: Single cell polarity in liquid phase facilitates tumour metastasis

doi: 10.1038/s41467-018-03139-6

Figure Lengend Snippet: Generic depolarisation decreases transmigration and seeding. a Polarity assays from 30 min (polarised) and 3 h (depolarised) time points from Fig. ( n = 6, paired t -test). b Transmigration assays of polarised (30 min) and depolarised (3 h) SkMel2 cells through HUVEC after 4, 7 or 24 h ( n = 3, one-sample t -tests compared to 100). Further transmigration assays are shown in Supplementary Fig. . c Adhesion assays of polarised (30 min) and depolarised (3 h) ezrin-GFP-expressing SkMel2 cells settling onto plastic. The area per cell was measured at the indicated times in >110 cells from at least 3 independent experiments (unpaired t -tests). d Individual (top) and averaged (bottom) adhesion kinetics of single polarised ( n = 48, red) and unpolarised ( n = 30, blue) ezrin-GFP-expressing SkMel2 cells within one, untreated population. Polarisation prior to adhesion was assessed at time point 0. The area per cell was measured at the indicated times (unpaired t -tests). e Adhesion of polarised and depolarised SkMel2 cells measured simultaneously in flow chambers after 30 min. Cells were unlabelled (white) or labelled with CellTracker green (green). In all, 70–380 cells were analysed per measurement ( n = 4, one-sample t -test compared to 50). f , h Polarity assays of ezrin-GFP-expressing U87 ( f ) and SNU-1 ( h ) cells at 30 min (polarised) and 3 h (depolarised) time points ( n = 6, paired t -test). g , i Transmigration assays of polarised (30 min) and depolarised (3 h) U87 cells ( g ) through HUVEC after 4, 7 or 24 h and of SNU-1 cells ( i ) after 5, 8 or 24 h through membrane ( n = 3 ( g ), n = 4 ( i ), one-sample t -tests compared to 100). j 3D reconstruction of GFP stainings from 30 serial 2 µm sections (right) of mouse lungs 30 min after injection with polarised or depolarised ezrin-GFP-expressing SkMel2 cells (Supplementary Movies and ). Grid length: 100 µm. Scale bars: 100 µm, arrowheads: GFP-positive cells. k – m Quantification of GFP-positive SkMel2 ( k ), U87 ( l ) and SNU-1 ( m ) cells from histological slides of mouse lungs as shown in j and Supplementary Fig. c, f by GFP-positive area per haematoxylin-positive area ( n = 10 ( k ), n = 7–8 ( l ), n = 13–15 ( m ), unpaired t -tests, normalised to the average of 'polarised' in m ). Further quantifications are shown in Supplementary Fig. . All data are represented as mean ± SD

Article Snippet: Female C57BL/6 mice of 8–10 weeks (Charles River Laboratories, Germany) were intravenously injected with 5 × 10 5 SkMel2 (ezrin-GFP), U87 (GFP) or SNU-1 (GFP) cells either polarised (30 min) or depolarised (3 h after detachment) or with 1.5 × 10 6 B16-F1, B16-F1 Mcam kd (M1), B16-F1 Mcam kd (M2), B16-F1 n.t. (expressing non-targeting shRNA control), B16-F0, B16-F0 GFP, B16-F0 Mcam or B16-F0 McamΔKKGK cells in random order.

Techniques: Transmigration Assay, Expressing, Membrane, Injection

Journal: bioRxiv

Article Title: PRMT activity promotes global 3’ UTR shortening in proliferating cells

doi: 10.1101/2025.03.06.641848

Figure Lengend Snippet: a) Violin plot showing proximal to distal usage shifts across each class of significant APA event. Proximal to distal usage shift is calculated as: dPA change in usage - pPA change in usage. White square = median. b) Scatter plots displaying Pearson correlation (r) of DMAi-induced poly(A) site usage change between different cell lines. Upper left = LU-99 vs MCF7, Lower left = NCI-H838 vs SUM149PT, Upper right = PANC0403 vs GP2D. Lower right = HCT116 p53 +/+ vs U2OS. c) Distribution of proximal poly(A) usage across all genes in a patient-derived lung tumour organoid model versus normal lung tissue organoids derived from the same patient. Scale: 0 = 0% usage, 1 = 100% usage. Statistical significance was calculated using the Kruskal-Wallis Test. d) An example of a 3’ UTR ( Prkca) whose shortening upon T cell activation (blue) is prevented by DMAi (red).

Article Snippet: GP2D, NCI-H838, LU-99, PANC0403, SK-MEL-2, SUM149PT and U2OS cells were sourced from the AstraZeneca Global Cell Bank.

Techniques: Derivative Assay, Activation Assay

Journal: bioRxiv

Article Title: PRMT activity promotes global 3’ UTR shortening in proliferating cells

doi: 10.1101/2025.03.06.641848

Figure Lengend Snippet: a) Upper = Scatter plots displaying Pearson correlation (r) in poly(A) site usage change triggered by DMAi versus siPCF11 (left) and CPSF73i (right). Lower = Pearson correlation (r) in poly(A) site usage change triggered by DMAi versus all other APA-inducing perturbation datasets within the 3’ RNA-seq panel. b) Comparison of position-dependent frequency of occurrence of GU-rich motifs within proximal and distal regions at DMAi-lengthened (red), non-DMAi-lengthened (green) and control (grey) sites. Running averages were calculated over 15 consecutive nucleotide positions. GU-rich motif = any 4mer combination of 2Gs + 2Us. c) Comparison of position-dependent frequency of occurrence of GU-rich motifs within proximal and distal regions at DMAi-lengthened (red) and unchanged, control (grey) 3’ UTRs, across three representative cancer lines. Upper = GP2D, Middle = HCT116 p53 +/+, Lower = PANC0403. d) CSTF2 eCLIP binding around poly(A) sites in 3’ UTRs across DMAi-vs non-DMAi-lengthened transcripts (expression matched), calculated from ENCODE consortium data in HepG2 cells. e) Distribution of % GC content within each gene region among DMAi-lengthened (red), non-DMAi-lengthened (green) and control (grey) genes. f) Distribution of baseline proximal poly(A) site usage in control (grey), DMAi-lengthened (red) and non-DMAi-lengthened (green) categories (expression matched). Scale: 0 = 0% usage, 1 = 100% usage. Statistical significance was calculated using the Kruskal-Wallis Test, with Bonferroni method p value adjustment for multiple testing. g) Boxplot showing the nucleotide distance between proximal and distal poly(A) sites at control (grey), DMAi-lengthened (red) and non-DMAi-lengthened (green) sites. Statistical significance was calculated using the Kruskal-Wallis Test, with Bonferroni method p value adjustment for multiple testing.

Article Snippet: GP2D, NCI-H838, LU-99, PANC0403, SK-MEL-2, SUM149PT and U2OS cells were sourced from the AstraZeneca Global Cell Bank.

Techniques: RNA Sequencing, Comparison, Control, Binding Assay, Expressing