human a375 malignant melanoma cells  (ATCC)

Journal: bioRxiv

Article Title: Distinct principles of genome compartmentalization in Drosophila and humans revealed by osmotic stress

doi: 10.64898/2026.04.02.716189

Figure Lengend Snippet: A. Human A375 cells immuno-stained with CTCF (magenta) and counterstained using DAPI. In control cells (top panel), grown in normal media, CTCF appears uniformly distributed on chromatin. In stress cells (middle panel), grown in media containing 250mM NaCl for 1 hour, chromatin appears highly condensed (inset) and occupancy of CTCF on chromatin is reduced, as it migrates to the nucleolus, interchromosomal spaces and the nuclear periphery. In these cells, CTCF does not form visible condensates. Recovery cells (bottom panel) were first grown in media containing 250mM NaCl for 1 hour and then returned to physiological media for 1 hour. Recovery cells look similar to control cells as CTCF is uniformly distributed on the chromatin and chromatin condensation appears similar to control (inset). B. Comparison of chromatin volume (DAPI stained area) for media (control, N = 30), 250mM NaCl treated (stress, N = 30) and physiological media treatment after 250mM NaCl treatment (recovery, N=30). Significant difference (One-Way ANOVA followed by multiple comparisons) in chromatin volume exists between control and stress (p = 0.007), stress and recovery (p = 0.005) but not between control and recovery. C. Drosophila S2 cells are uniformly immuno-stained with dCTCF (magenta) in normal media (control, top panel). In response to 250mM NaCl treatment (stress), chromatin appears condensed (DAPI, inset). The occupancy of dCTCF on the chromatin is reduced as it forms insulator bodies and migrates to nucleoplasm spaces. Salt stress treated cells returned to physiological media (recovery) look similar to the control cells as dCTCF is uniformly distributed on the chromatin. Scale bar = 2µm D . Comparison of chromatin volume (DAPI stained area) for media (control, N= 30), 250mM NaCl treated (stress, N= 30) and media treatment after 250mM NaCl treatment (recovery, N= 30). A significant difference exists in chromatin volume between control and stress (p <0.001), control and recovery (p <0.001) but not between stress and recovery. Scale bars = 2 µm.

Article Snippet: The human A375 malignant melanoma cells were purchased from ATCC (ATCC® CRL-1619TM).

Techniques: Staining, Control, Comparison

Journal: bioRxiv

Article Title: Distinct principles of genome compartmentalization in Drosophila and humans revealed by osmotic stress

doi: 10.64898/2026.04.02.716189

Figure Lengend Snippet: A. A 1Mb binned heatmap of human A375 cells (top panel) and Drosophila S2 cells (bottom panel) across the 3 conditions. B . 1.0 Mb resolution log2ratio whole genome heatmaps of human A375 Stress versus Control (left panel), Recovery versus Control (middle panel), and Recovery versus Stress (right panel). Insets of chromosomes 1 and 2 are placed below their respective heatmaps. C. 1.0 Mb log2ratio whole genome heatmaps of Drosophila S2 Stress versus Control (left panel), Recovery versus Control (middle panel), and Recovery versus Control (right panel). Insets of chromosome 2L and 2R are placed below their respective heatmaps. D. A scaling plot showing contact decay with distance across all chromosomes at a 250 kb bin size in human A375 cells. E . A scaling plot showing contact decay with distance across all chromosomes at a 1Mb bin size in Drosophila cells

Article Snippet: The human A375 malignant melanoma cells were purchased from ATCC (ATCC® CRL-1619TM).

Techniques: Control

Journal: bioRxiv

Article Title: Distinct principles of genome compartmentalization in Drosophila and humans revealed by osmotic stress

doi: 10.64898/2026.04.02.716189

Figure Lengend Snippet: A. Heatmaps of genomic contacts (250kb resolution) of chromosome 18: 20Mb-70Mb of human A375 media treated, 250mM NaCl treated and recovery. The first principal component, aligned below each matrix, shows compartment classification into A (red) and B (blue) compartments. B. Heatmaps of genomic contacts (20 kb resolution) of chromosome 2L:14Mb-20Mb of Drosophila S2 media treated, 250mM NaCl treated and recovery are shown. The first principal component, showing compartment identity, is aligned below each heatmap as in (A). C. Genome-wide Pearson’s correlation of first principal component values for human (top panel) or Drosophila (bottom panel) comparing control versus stress (far left panel), control versus recovery (middle panel), and stress versus recovery (far right panel). The lines of best-fit are shown in blue through the data points. The blue lines through the data points indicate the lines of best fit.

Article Snippet: The human A375 malignant melanoma cells were purchased from ATCC (ATCC® CRL-1619TM).

Techniques: Genome Wide, Control

Journal: bioRxiv

Article Title: Distinct principles of genome compartmentalization in Drosophila and humans revealed by osmotic stress

doi: 10.64898/2026.04.02.716189

Figure Lengend Snippet: A. For A375 cells, the left panel shows the number of 250 kb bins and percent of the whole genome that switch compartments, as defined by a PC1 sign change and at least a 10% shift in PC1 value. Given these compartment switch bins, the middle panel shows the proportion that revert fully (green), partially (yellow), or not at all (grey) upon return to control conditions. “Recovered” is defined as a Recovery condition PC1 value within 2% of the Control value while “Not Recovered” bins have a Recovery PC1 value within 2% of the Stress value. The patterns of PC1 value change are shown in the graphs at right, where each line represents the trajectory of one genomic bin. B. Same analysis as in A but for Drosophila S2 cells C. Saddle plots generated from 250Kb and 20kb binned distance corrected Z-score matrices for chromosome 18 of human A375 cells (top panel) and chromosome 2L of Drosophila S2 cells (bottom panel) respectively. The binned matrices in each case are reordered from strongest B to strongest A compartment identity. The binned matrices were smoothed to 500Kb for the human A375 cells while the Drosophila S2 cell genome was smoothed at 20kb. D. Saddle plots showing comparison of A and B compartment interaction strengths in different conditions for human A375 cells (top) and Drosophila S2 cells (bottom). The Z-score interaction strengths were subtracted between the indicated conditions and the differences are shown. E. Compartment strength recovers in A375 much more than in S2 cells. The compartment strength for each condition in each cell type is calculated as (AA+BB)/AB. Where AA, for example, is the sum of all interactions within the top 20% of A compartment bins: the bottom right corner of the saddle plots.

Article Snippet: The human A375 malignant melanoma cells were purchased from ATCC (ATCC® CRL-1619TM).

Techniques: Control, Generated, Comparison

Journal: bioRxiv

Article Title: Distinct principles of genome compartmentalization in Drosophila and humans revealed by osmotic stress

doi: 10.64898/2026.04.02.716189

Figure Lengend Snippet: A. Heatmaps showing human A375 TAD structures (called at 40kb) at chr1:180.2 - 183 Mb. B. Heatmaps showing Drosophila S2 cell TAD structures (called at 5kb) at chr3L:10.6 - 11 Mb. C. Log 2 Ratio of aggregate contact maps at TAD boundaries called at 40 kb bins in A375 cells. D. Log 2 Ratio of average TAD boundary (called at 5kb) plots from S2 cells. E. Human A375 cell comparison of TAD boundary strength scores. P-values less than 0.05 are deemed significant. F. Comparison of TAD boundary strength score in Drosophila S2 cells. P-values are generated by one-way ANOVA and values less than 0.05 are deemed significant. C-F . Boundary strengths were derived from the cworld-dekker method to calculate insulation scores. G-H. Comparison of numbers of detected TAD boundaries in human A375 cells (G) or Drosophila S2 cells (H) derived from the insulation scores. P-values were generated using Fisher’s exact test for each pair of conditions, with values less than 0.05 considered statistically significant.

Article Snippet: The human A375 malignant melanoma cells were purchased from ATCC (ATCC® CRL-1619TM).

Techniques: Comparison, Generated, Derivative Assay, Insulation

Journal: Journal of Cellular and Molecular Medicine

Article Title: CircANKRD52 Augments the Growth and Invasion of Melanoma Cells by Sponging miR ‐141‐3p and Upregulating PRKACB

doi: 10.1111/jcmm.70909

Figure Lengend Snippet: Identification of a circANKRD52 in melanoma cells. (A) The genomic loci of circANKRD52. (B) RT‐qPCR analysis of the expression levels of circANKRD52 and ANKRD52 after treatment with RNase R in A375 and SK‐MEL‐28 cells. (C) RT‐qPCR analysis of the transcriptional stability of circANKRD52 and ANKRD52 after treatment with Actinomycin D in A375 cells. (D) RT‐qPCR analysis of the location of circANKRD52 in A375 and SK‐MEL‐28 cells. (E) FISH analysis of the location of circANKRD52 in A375 and SK‐MEL‐28 cells. Data shown are the mean ± SEM of three experiments. **** p < 0.0001.

Article Snippet: Human malignant melanoma cell lines A375, Hs294T, SK‐MEL‐28 were procured from American Type Culture Collection (ATCC, Manassas, VA, USA) and melanocytes were used as the control cells.

Techniques: Quantitative RT-PCR, Expressing

Journal: Journal of Cellular and Molecular Medicine

Article Title: CircANKRD52 Augments the Growth and Invasion of Melanoma Cells by Sponging miR ‐141‐3p and Upregulating PRKACB

doi: 10.1111/jcmm.70909

Figure Lengend Snippet: CircANKRD52 augments proliferation and invasion of melanoma cells. (A) EdU analysis of the cell proliferation activity after transfection with oe‐circANKRD52 into A375 cells or sh‐circANKRD52 into SK‐MEL‐28 cells. (B) Transwell analysis of the cell invasion capabilities after transfection with oe‐circANKRD52 into A375 cells or sh‐circANKRD52 into SK‐MEL‐28 cells. (C) Flow cytometry analysis of the cell apoptosis after transfection with oe‐circANKRD52 into A375 cells or sh‐circANKRD52 into SK‐MEL‐28 cells. (D) Tube formation assay analysis of the angiogenesis ability after transfection with oe‐circANKRD52 into A375 cells or sh‐circANKRD52 into SK‐MEL‐28 cells. (E) Western blot analysis of the protein levels of VEGF after transfection with oe‐circANKRD52 into A375 cells or sh‐circANKRD52 into SK‐MEL‐28 cells. Data shown are the mean ± SEM of three experiments. * p < 0.05.

Article Snippet: Human malignant melanoma cell lines A375, Hs294T, SK‐MEL‐28 were procured from American Type Culture Collection (ATCC, Manassas, VA, USA) and melanocytes were used as the control cells.

Techniques: Activity Assay, Transfection, Flow Cytometry, Tube Formation Assay, Western Blot

Journal: Journal of Cellular and Molecular Medicine

Article Title: CircANKRD52 Augments the Growth and Invasion of Melanoma Cells by Sponging miR ‐141‐3p and Upregulating PRKACB

doi: 10.1111/jcmm.70909

Figure Lengend Snippet: The circANKRD52 acts as a sponge of miR‐141‐3p in melanoma cells. (A) The RNA pull‐down analysis of the binding between circANKRD52 probe and miRNA in A375 cells. (B) RT‐qPCR analysis of the expression levels of miR‐141‐3p in melanoma and the adjacent normal tissues. (C) Pearson's correlation analysis of the correlation between miR‐141‐3p and circANKRD52 in melanoma tissues. (D) RT‐qPCR analysis of the expression of miR‐141‐3p in melanoma cell lines (A375, Hs294T, and SK‐MEL‐28). (E) The dual luciferase reporter assay indicated the binding between circANKRD52 3′UTR and miR‐141‐3p. (F) RT‐qPCR analysis of the expression of miR‐141‐3p after transfection with oe‐circANKRD52 into A375 cells or sh‐circANKRD52 into SK‐MEL‐28 cells. (G) RIP analysis of the binding ability between circANKRD52 and Ago2 after transfection with oe‐circANKRD52 into A375 cells or sh‐circANKRD52 into SK‐MEL‐28 cells. (H) RNA pull‐down assay analysis of the binding between Bio‐circANKRD52 WT and miR‐141‐3p. Data shown are the mean ± SEM of three experiments. * p < 0.05.

Article Snippet: Human malignant melanoma cell lines A375, Hs294T, SK‐MEL‐28 were procured from American Type Culture Collection (ATCC, Manassas, VA, USA) and melanocytes were used as the control cells.

Techniques: Binding Assay, Quantitative RT-PCR, Expressing, Luciferase, Reporter Assay, Transfection, Pull Down Assay

Journal: Journal of Cellular and Molecular Medicine

Article Title: CircANKRD52 Augments the Growth and Invasion of Melanoma Cells by Sponging miR ‐141‐3p and Upregulating PRKACB

doi: 10.1111/jcmm.70909

Figure Lengend Snippet: The miR‐141‐3p reverses circANKRD52‐induced melanoma cell proliferation and invasion. (A) EdU analysis of the cell proliferation activity after co‐transfection with oe‐circANKRD52 and miR‐141‐3p mimic into A375 cells or sh‐circANKRD52 and miR‐141‐3p inhibitor into SK‐MEL‐28 cells. (B) Transwell analysis of the cell invasion capabilities after co‐transfection with oe‐circANKRD52 and miR‐141‐3p mimic into A375 cells or sh‐circANKRD52 and miR‐141‐3p inhibitor into SK‐MEL‐28 cells. (C) Flow cytometry analysis of the cell apoptosis after co‐transfection with oe‐circANKRD52 and miR‐141‐3p mimic into A375 cells or sh‐circANKRD52 and miR‐141‐3p inhibitor into SK‐MEL‐28 cells. (D) Tube formation assay analysis of the angiogenesis ability after co‐transfection with oe‐circANKRD52 and miR‐141‐3p mimic into A375 cells or sh‐circANKRD52 and miR‐141‐3p inhibitor into SK‐MEL‐28 cells. (E) Western blot analysis of the protein levels of VEGF after co‐transfection with oe‐circANKRD52 and miR‐141‐3p mimic into A375 cells or sh‐circANKRD52 and miR‐141‐3p inhibitor into SK‐MEL‐28 cells. Data shown are the mean ± SEM of three experiments. * p < 0.05.

Article Snippet: Human malignant melanoma cell lines A375, Hs294T, SK‐MEL‐28 were procured from American Type Culture Collection (ATCC, Manassas, VA, USA) and melanocytes were used as the control cells.

Techniques: Activity Assay, Cotransfection, Flow Cytometry, Tube Formation Assay, Western Blot

Journal: Journal of Cellular and Molecular Medicine

Article Title: CircANKRD52 Augments the Growth and Invasion of Melanoma Cells by Sponging miR ‐141‐3p and Upregulating PRKACB

doi: 10.1111/jcmm.70909

Figure Lengend Snippet: PRKACB is identified as a direct target of miR‐141‐3p in melanoma cells. (A) RT‐qPCR analysis of the PRKACB expression in melanoma and the adjacent normal tissues. (B) Pearson's correlation analysis of the correlations of PRKACB with miR‐141‐3p or circANKRD52 expression in melanoma tissues. (C, D) RT‐qPCR and Western blot analysis of the expression of PRKACB in A375, SK‐MEL‐28, and melanocytes. (E) The dual luciferase reporter assay indicated the binding between miR‐141‐3p and PRKACB 3'UTR. (F) RT‐qPCR analysis of the expression of PRKACB after transfection with oe‐circANKRD52 into A375 cells or sh‐circANKRD52 into SK‐MEL‐28 cells. (G) RT‐qPCR analysis of the expression of PRKACB after transfection with miR‐141‐3p mimic into A375 cells or miR‐141‐3p inhibitor into SK‐MEL‐28 cells. Data shown are the mean ± SEM of three experiments. * p < 0.05. # p < 0.05.

Article Snippet: Human malignant melanoma cell lines A375, Hs294T, SK‐MEL‐28 were procured from American Type Culture Collection (ATCC, Manassas, VA, USA) and melanocytes were used as the control cells.

Techniques: Quantitative RT-PCR, Expressing, Western Blot, Luciferase, Reporter Assay, Binding Assay, Transfection

Journal: Journal of Cellular and Molecular Medicine

Article Title: CircANKRD52 Augments the Growth and Invasion of Melanoma Cells by Sponging miR ‐141‐3p and Upregulating PRKACB

doi: 10.1111/jcmm.70909

Figure Lengend Snippet: The circANKRD52/PRKACB axis mediates melanoma cell proliferation and invasion. (A) EdU analysis of the cell proliferation activity after co‐transfection with oe‐circANKRD52 and sh‐PRKACB into A375 cells or sh‐circANKRD52 and oe‐PRKACB into SK‐MEL‐28 cells. (B) Transwell analysis of the cell invasion capabilities after co‐transfection with oe‐circANKRD52 and sh‐PRKACB into A375 cells or sh‐circANKRD52 and oe‐PRKACB into SK‐MEL‐28 cells. (C) Flow cytometry analysis of the cell apoptosis after co‐transfection with oe‐circANKRD52 and sh‐PRKACB into A375 cells or sh‐circANKRD52 and oe‐PRKACB into SK‐MEL‐28 cells. (D) Tube formation assay analysis of the angiogenesis ability after co‐transfection with oe‐circANKRD52 and sh‐PRKACB into A375 cells or sh‐circANKRD52 and oe‐PRKACB into SK‐MEL‐28 cells. (E) Western blot analysis of the protein levels of VEGF after co‐transfection with oe‐circANKRD52 and sh‐PRKACB into A375 cells or sh‐circANKRD52 and oe‐PRKACB into SK‐MEL‐28 cells. Data shown are the mean ± SEM of three experiments. * p < 0.05.

Article Snippet: Human malignant melanoma cell lines A375, Hs294T, SK‐MEL‐28 were procured from American Type Culture Collection (ATCC, Manassas, VA, USA) and melanocytes were used as the control cells.

Techniques: Activity Assay, Cotransfection, Flow Cytometry, Tube Formation Assay, Western Blot