off target cell line  (ATCC)

Journal: Bioactive Materials

Article Title: Multimodal profiling of CAR T cells against glioblastoma using a microengineered 3D tumor-on-a-chip model

doi: 10.1016/j.bioactmat.2026.01.003

Figure Lengend Snippet: Off-target cytotoxicity evaluation of CAR T cells using the 3D GOC system. A) Schematic representation of the differing cytolytic mechanisms of UTD, TV-13, and IL-13 CAR T cells against IL13Rα1 + HT-1080 tumor cells. Created with BioRender.com . B) Flow cytometric analysis confirming IL13Rα1 and mCherry (reporter gene) expression on IL13Rα1 + HT-1080 tumor cells. Antigen expression (IL13Rα1 or mCherry) on viable tumor cells shown in histograms: blue for IL13Rα1 + HT-1080 tumor cells and red for control tumor cells. The values within each histogram indicate the percentage of positive cells, with the mean fluorescence intensity (MFI) shown in parentheses. C) Microfluidic evaluation of off-target toxicities of T cells. (i) Representative tile images of tumor-stroma interface stained for actin cytoskeleton (green), showing differences in migration of IL13R1 + HT-1080 tumor cells (red) within the 3D GOC model across varying densities of UTD, TV-13 CAR, and IL-13 CAR T cells. (ii) Quantification of the migration distance of the IL13Rα1 + HT-1080 tumor cells in response to varying T cell concentrations. Data are represented as mean ± SD measured from three biological replicates ( n = 3) , T cell donors: DN18, DN28, and DN31, ∗ p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗ ∗p < 0.0001. Two-way ANOVA with Tukey's multiple comparisons test was utilized for statistical analysis. (iii) Bar graph showing the difference in nuclei per field of view (FOV) across different T cell densities, used as a measure of chain migration by IL13Rα1 + HT-1080 tumor cells. Data are represented as mean ± SD measured from three biological replicates ( n = 3) , T cell donors: DN18, DN28, and DN31, ∗ p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001. Two-way ANOVA with Tukey's multiple comparisons test was utilized for statistical analysis, and (iv) Bar graph representing the percentage of T cells positive for intracellular cytokines in the presence of IL13Rα1 + HT-1080 tumor cells. Data are represented as mean ± SD measured from three biological replicates ( n = 3) , ∗ p < 0.05, ∗∗p < 0.01, ∗∗∗ ∗p < 0.0001. Two-way ANOVA with Tukey's multiple comparisons test was utilized for statistical analysis.

Article Snippet: HT-1080 Culture : Human fibrosarcoma cells (CCL-121, ATCC or HT-1080) were used to generate an off-target cell line (IL13Rα1 + HT-1080) expressing IL13Rα1-T2A-mCherry gene, which was single-sorted for the experiments described here.

Techniques: Gene Expression, Expressing, Control, Fluorescence, Staining, Migration

Journal: Bioactive Materials

Article Title: Multimodal profiling of CAR T cells against glioblastoma using a microengineered 3D tumor-on-a-chip model

doi: 10.1016/j.bioactmat.2026.01.003

Figure Lengend Snippet: Off-target cytotoxicity evaluation of CAR T cells using the 3D GOC system. A) Schematic representation of the differing cytolytic mechanisms of UTD, TV-13, and IL-13 CAR T cells against IL13Rα1 + HT-1080 tumor cells. Created with BioRender.com . B) Flow cytometric analysis confirming IL13Rα1 and mCherry (reporter gene) expression on IL13Rα1 + HT-1080 tumor cells. Antigen expression (IL13Rα1 or mCherry) on viable tumor cells shown in histograms: blue for IL13Rα1 + HT-1080 tumor cells and red for control tumor cells. The values within each histogram indicate the percentage of positive cells, with the mean fluorescence intensity (MFI) shown in parentheses. C) Microfluidic evaluation of off-target toxicities of T cells. (i) Representative tile images of tumor-stroma interface stained for actin cytoskeleton (green), showing differences in migration of IL13R1 + HT-1080 tumor cells (red) within the 3D GOC model across varying densities of UTD, TV-13 CAR, and IL-13 CAR T cells. (ii) Quantification of the migration distance of the IL13Rα1 + HT-1080 tumor cells in response to varying T cell concentrations. Data are represented as mean ± SD measured from three biological replicates ( n = 3) , T cell donors: DN18, DN28, and DN31, ∗ p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗ ∗p < 0.0001. Two-way ANOVA with Tukey's multiple comparisons test was utilized for statistical analysis. (iii) Bar graph showing the difference in nuclei per field of view (FOV) across different T cell densities, used as a measure of chain migration by IL13Rα1 + HT-1080 tumor cells. Data are represented as mean ± SD measured from three biological replicates ( n = 3) , T cell donors: DN18, DN28, and DN31, ∗ p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001. Two-way ANOVA with Tukey's multiple comparisons test was utilized for statistical analysis, and (iv) Bar graph representing the percentage of T cells positive for intracellular cytokines in the presence of IL13Rα1 + HT-1080 tumor cells. Data are represented as mean ± SD measured from three biological replicates ( n = 3) , ∗ p < 0.05, ∗∗p < 0.01, ∗∗∗ ∗p < 0.0001. Two-way ANOVA with Tukey's multiple comparisons test was utilized for statistical analysis.

Article Snippet: HT-1080 Culture : Human fibrosarcoma cells (CCL-121, ATCC or HT-1080) were used to generate an off-target cell line (IL13Rα1 + HT-1080) expressing IL13Rα1-T2A-mCherry gene, which was single-sorted for the experiments described here.

Techniques: Gene Expression, Expressing, Control, Fluorescence, Staining, Migration

Journal: Bioactive Materials

Article Title: Multimodal profiling of CAR T cells against glioblastoma using a microengineered 3D tumor-on-a-chip model

doi: 10.1016/j.bioactmat.2026.01.003

Figure Lengend Snippet: Off-target cytotoxicity evaluation of CAR T cells using the 3D GOC system. A) Schematic representation of the differing cytolytic mechanisms of UTD, TV-13, and IL-13 CAR T cells against IL13Rα1 + HT-1080 tumor cells. Created with BioRender.com . B) Flow cytometric analysis confirming IL13Rα1 and mCherry (reporter gene) expression on IL13Rα1 + HT-1080 tumor cells. Antigen expression (IL13Rα1 or mCherry) on viable tumor cells shown in histograms: blue for IL13Rα1 + HT-1080 tumor cells and red for control tumor cells. The values within each histogram indicate the percentage of positive cells, with the mean fluorescence intensity (MFI) shown in parentheses. C) Microfluidic evaluation of off-target toxicities of T cells. (i) Representative tile images of tumor-stroma interface stained for actin cytoskeleton (green), showing differences in migration of IL13R1 + HT-1080 tumor cells (red) within the 3D GOC model across varying densities of UTD, TV-13 CAR, and IL-13 CAR T cells. (ii) Quantification of the migration distance of the IL13Rα1 + HT-1080 tumor cells in response to varying T cell concentrations. Data are represented as mean ± SD measured from three biological replicates ( n = 3) , T cell donors: DN18, DN28, and DN31, ∗ p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗ ∗p < 0.0001. Two-way ANOVA with Tukey's multiple comparisons test was utilized for statistical analysis. (iii) Bar graph showing the difference in nuclei per field of view (FOV) across different T cell densities, used as a measure of chain migration by IL13Rα1 + HT-1080 tumor cells. Data are represented as mean ± SD measured from three biological replicates ( n = 3) , T cell donors: DN18, DN28, and DN31, ∗ p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001. Two-way ANOVA with Tukey's multiple comparisons test was utilized for statistical analysis, and (iv) Bar graph representing the percentage of T cells positive for intracellular cytokines in the presence of IL13Rα1 + HT-1080 tumor cells. Data are represented as mean ± SD measured from three biological replicates ( n = 3) , ∗ p < 0.05, ∗∗p < 0.01, ∗∗∗ ∗p < 0.0001. Two-way ANOVA with Tukey's multiple comparisons test was utilized for statistical analysis.

Article Snippet: HT-1080 Culture : Human fibrosarcoma cells (CCL-121, ATCC or HT-1080) were used to generate an off-target cell line (IL13Rα1 + HT-1080) expressing IL13Rα1-T2A-mCherry gene, which was single-sorted for the experiments described here.

Techniques: Gene Expression, Expressing, Control, Fluorescence, Staining, Migration

Journal: Scientific Reports

Article Title: Heat shock factor-1 alleviates ER-stress in Caenorhabditis elegans

doi: 10.1038/s41598-026-43060-3

Figure Lengend Snippet: HSF1 is required for the proper induction of UPR ER genes in human cell lines. ( a ) and ( b ) Venn diagrams showing that genes upregulated upon tunicamycin treatment , significantly overlap (RF: 1.86; p < 2.35e−06 and RF: 1.75; p < 3.83e−13 respectively) with genes directly activated by HSF1 in human cell lines . ( c ) Table showing a selected list of HSF1 target genes that are also upregulated by tunicamycin treatment based on two separate published RNAseq experiments , . ( d ) Activation of XBP1 splicing and induction of HSPA5 ( BIP ) mRNA levels depends on HSF1 upon heat shock in HT-1080 cell line. ( e ) Activation of XBP1 splicing and induction of HSPA5 ( BIP ) mRNA levels depends on HSF1 upon tunicamycin induced ER stress in HT-1080 cell line. Data of three experiments were plotted with error bars indicating the SD. p values were determined by two-tailed, unpaired t-test; * = p < 0.05, ** = p < 0.01, *** = p < 0.001, ns = not significant; SD = standard deviation. Source data underlying panels a–c are provided in Supplementary Table Source data underlying panels d and e are provided in Supplementary Table .

Article Snippet: HT-1080 and HEK-293T human cell lines (ATCC, Manassas, VA, USA) were cultured according to ATCC guidelines.

Techniques: RNA sequencing, Activation Assay, Two Tailed Test, Standard Deviation

Journal: Nucleic Acids Research

Article Title: MDS/AML-associated DDX41 helicase facilitates homologous recombination repair by potentially resolving R-loops

doi: 10.1093/nar/gkag219

Figure Lengend Snippet: DDX41 loss alters cell survival against genotoxic stress. ( A ) Western blot assays of WT and DDX41–KO HT1080 cell lines with a DDX41 antibody. β-Actin serves as a loading control. ( B–D ) Cell survival assays of WT and DDX41–KO HT1080 cells treated with bleomycin (B), camptothecin (C), or UV (D). ( E and F ) Immunofluorescence of endogenous DDX41 (E) and GFP tagged DDX41 (F) in HT1080 cells post-bleomycin treatment (30 μg/ml for 1 h). Quantification of DDX41 foci is shown at the bottom. The number of foci was calculated manually using 30 cells per individual panel from three independent experiments. UT, untreated with DNA damage. Data represent the mean ± SEM of three independent experiments; * P < 0.05.

Article Snippet: HeLa (CCL-2) and HT1080 (CCL-121, both from ATCC) cells were grown in Dulbecco’s modified Eagle medium (DMEM, 11995065, Gibco) supplemented with 10% fetal bovine serum (F1051, Sigma) and penicillin/streptomycin (100 U/ml each, P4333, Sigma).

Techniques: Western Blot, Control, Immunofluorescence

Journal: Nucleic Acids Research

Article Title: MDS/AML-associated DDX41 helicase facilitates homologous recombination repair by potentially resolving R-loops

doi: 10.1093/nar/gkag219

Figure Lengend Snippet: Increased DSBs in DDX41–KO cells. ( A and B ) Fluorescent microscopy analysis of HT1080 cells (WT and DDX41–KO) stained with DDX41 and γH2AX (A) or 53BP1 antibody (B), and DAPI (blue) at 4 h post-bleomycin treatment (30 μg/ml for 1 h). Quantification of γH2AX or 53BP1 foci is shown on the right. The number of foci were calculated using 30 cells per individual panel in ImageJ. ( C ) Neutral comet assays of HT1080 cells (WT and DDX41–KO) at 4 h post-bleomycin treatment (30 μg/ml for 1 h). Quantification of comet moments is shown on the right. The value of comet moments were calculated using 30 cells per individual panel by ImageJ. ( D ) Western blot assays of HT1080 cell lines (WT and DDX41–KO) after bleomycin treatment (30 μg/ml for 1 h) with indicated antibodies. β-Actin serves as a loading control. Quantification of the relative level of γH2AX, p-BRCA1, and DDX41 is shown below. Data represent the mean ± SEM of three independent experiments; *** P < 0.001. UT, untreated with DNA damage.

Article Snippet: HeLa (CCL-2) and HT1080 (CCL-121, both from ATCC) cells were grown in Dulbecco’s modified Eagle medium (DMEM, 11995065, Gibco) supplemented with 10% fetal bovine serum (F1051, Sigma) and penicillin/streptomycin (100 U/ml each, P4333, Sigma).

Techniques: Microscopy, Staining, Western Blot, Control

Journal: Nucleic Acids Research

Article Title: MDS/AML-associated DDX41 helicase facilitates homologous recombination repair by potentially resolving R-loops

doi: 10.1093/nar/gkag219

Figure Lengend Snippet: Increased R-loops in DDX41–KO cells. ( A ) Dot blot analysis of nucleic acids with S9.6 antibody (top) or dsDNA antibody (bottom) with or without RNase H treatment after HT1080 cells (WT and DDX41–KO) treated with bleomycin (30 μg/ml for 1 h). Quantification of S9.6/dsDNA is shown on the right. UT, untreated with DNA damage. ( B ) Immunofluorescence staining with DDX41 and S9.6 antibodies with or without RNase H treatment in HT1080 cells (WT and DDX41–KO) post BLM treatment (30 μg/ml for 1 h). Quantification of S9.6 foci is shown on the right. Data represent the mean ± SD of three independent experiments for (A) and (B). ns, not significant ( P ≥ 0.05); * P < 0.05, ** P < 0.01, and *** P < 0.001.

Article Snippet: HeLa (CCL-2) and HT1080 (CCL-121, both from ATCC) cells were grown in Dulbecco’s modified Eagle medium (DMEM, 11995065, Gibco) supplemented with 10% fetal bovine serum (F1051, Sigma) and penicillin/streptomycin (100 U/ml each, P4333, Sigma).

Techniques: Dot Blot, Immunofluorescence, Staining

Journal: Nucleic Acids Research

Article Title: MDS/AML-associated DDX41 helicase facilitates homologous recombination repair by potentially resolving R-loops

doi: 10.1093/nar/gkag219

Figure Lengend Snippet: DDX41 interacts with R-loops and colocalizes with γH2AX. ( A ) Dot blot analysis of nucleic acids with the S9.6 antibody after HT1080 cells (WT and DDX41–KO) treated with or without bleomycin (30 μg/ml for 1 h) and immunoprecipitated with a DDX41 antibody or normal mouse IgG; IB, immunoblotting. ( B ) Co-IP of DDX41 protein by the S9.6 antibody in HT1080 cells (WT and DDX41–KO) that were treated with or without bleomycin (30 μg/ml for 1 h) and blotted with a DDX41 antibody. Normal mouse IgG was used as a control; IP, immunoprecipitation. ( C ) Representative images of PLA between DDX41 and S9.6 in HT1080 cells (WT and DDX41–KO) that were treated with or without bleomycin (30 μg/ml for 1 h) and quantification of PLA signal (right panel). Thirty cells were counted in each PLA by ImageJ. ( D ) Immunofluorescence staining of WT HT1080 cells with DDX41 (green), γH2AX (red), and DAPI (blue) at 4 h after bleomycin treatment (30 μg/ml for 1 h) or untreated (UT). Quantification of colocalization with Pearson’s correlation coefficient is shown on the right. The Pearson’s correlation coefficient was obtained using the JACoP plugin in ImageJ for at least 30 cells. ( E ) Representative images of PLA between DDX41 and γH2AX or 53BP1 in HT1080 cells (WT and DDX41–KO) that were treated with bleomycin (30 μg/ml for 1 h) and quantification of PLA signal (right panel). Data represent the mean ± SEM of three independent experiments. ns, not significant ( P ≥ 0.05), *** P < 0.001.

Article Snippet: HeLa (CCL-2) and HT1080 (CCL-121, both from ATCC) cells were grown in Dulbecco’s modified Eagle medium (DMEM, 11995065, Gibco) supplemented with 10% fetal bovine serum (F1051, Sigma) and penicillin/streptomycin (100 U/ml each, P4333, Sigma).

Techniques: Dot Blot, Immunoprecipitation, Western Blot, Co-Immunoprecipitation Assay, Control, Immunofluorescence, Staining

Journal: Nucleic Acids Research

Article Title: MDS/AML-associated DDX41 helicase facilitates homologous recombination repair by potentially resolving R-loops

doi: 10.1093/nar/gkag219

Figure Lengend Snippet: DDX41 loss diminishes HR repair. ( A ) Western blot assays of DDX41 siRNA and siRNA control in U2OS GFP reporter cell lines with indicated antibodies. β-Actin serves as a loading control. Quantification of relative protein level for DDX41 and I-SecI is shown on the right. ( B ) Percentages of GFP positive cells as assessed by flow cytometry 36 h after U2OS GFP reporter cell lines treated with siRNA control, siRNA control + I-SceI plasmid, or DDX41 siRNA + I-SceI plasmid. ( C ) Cell survival assays of WT and DDX41–KO HT1080 cells treated with Olaparib. ( D and E ) Immunofluorescence staining of WT and DDX41–KO HT1080 cells with γH2AX, RPA32 (D) or RAD51 (E), and DAPI without bleomycin treatment (UT) or 4 h post BLM treatment (30 μg/ml for 1 h). Quantification of RPA32 and RAD51 foci is shown in the middle. Data represent the mean ± SEM of three independent experiments. * P < 0.05, *** P < 0.001, and **** P < 0.0001.

Article Snippet: HeLa (CCL-2) and HT1080 (CCL-121, both from ATCC) cells were grown in Dulbecco’s modified Eagle medium (DMEM, 11995065, Gibco) supplemented with 10% fetal bovine serum (F1051, Sigma) and penicillin/streptomycin (100 U/ml each, P4333, Sigma).

Techniques: Western Blot, Control, Flow Cytometry, Plasmid Preparation, Immunofluorescence, Staining