Journal: Bioactive Materials

Article Title: A novel CD44-targeting aptamer recognizes chemoresistant mesenchymal stem-like TNBC cells and inhibits tumor growth

doi: 10.1016/j.bioactmat.2025.04.027

Figure Lengend Snippet: Identification of the target of sTN58 aptamer on TNBC cell surface. (A) Schematic representation of biotin-sTN58-mediated affinity purification. Membrane-protein fraction from Cis-Pt-R cells were subjected to a preclearing step to remove non-specific components prior to the sTN58-mediated precipitation. The colloidal Blue-stained SDS-PAGE (10 %) displayed is utilized for the analysis of target purification mediated by the sTN58 aptamer. The molecular weights of protein markers are reported. Lane 1, molecular markers; lane 2, membrane extracts; lane 3, 15 μg aliquot of unbound proteins from SCR-mediated purification; lane 4, proteins captured with sTN58. Red boxes indicate the regions excised for MS analyses. (B) Comparison of transcript expression values of best candidates in different BC cell lines. The normalized transcript expression values (nTPM), according to HPA, are reported relative to MDA-MB-231 target cells, whose expression level is arbitrarily set to 1. Box indicates the 5 candidates chosen for experimental validation. (C) Immunoblot analysis of EphA2, CD44, integrin β1, myoferlin, liprin β1 and ZO-1, and of the housekeeping proteins α-tubulin and vinculin. The molecular weights of protein markers are reported. Black dashed lines delineate the boundary between non-contiguous lanes of the same gel. (D) The histogram shows the relative fold-change in expression levels of the indicated proteins compared to the housekeeping protein α-tubulin or vinculin, normalized to MDA-MB-231 target cells, whose expression level is arbitrarily set to 1. (E) Binding affinity (1/Kd) of TN58 aptamer to the indicated cell lines expressed relative to MDA-MB-231 target cells. Dose response curves and binding affinity calculations for MDA-MB-231 and Cis-Pt-R and Dox-R chemoresistant cells, as well as non-TNBC BT-474, MCF-7 and A431 cells were previously reported [ , ]. The dose response curve used for Kd calculation in relation to BT-549 is shown in . "NB", no binding.

Article Snippet: For cell binding of anti-CD44 antibody, 2.0 × 10 5 cells were left untreated or incubated for 20 min at RT with CD44 phycoerythrin (PE)-conjugated antibody (CD44-PE Ab, IM7, 0.25 μg/test, Santa Cruz Biotechnology) in DPBS supplemented with 0.1 % bovine serum albumin.

Techniques: Affinity Purification, Membrane, Staining, SDS Page, Purification, Comparison, Expressing, Biomarker Discovery, Western Blot, Binding Assay

Journal: Bioactive Materials

Article Title: A novel CD44-targeting aptamer recognizes chemoresistant mesenchymal stem-like TNBC cells and inhibits tumor growth

doi: 10.1016/j.bioactmat.2025.04.027

Figure Lengend Snippet: sTN58 binds to CD44-positive TNBC cell lines. Following 5 min incubation at RT with 2 μM Alexa 647-sTN58, Cis-Pt-R (A) or BT-474 (B) cells were stained with CD44 Ab, visualized by confocal microscopy, and photographed. Alexa 647-SCR was used as a negative control. Alexa 647-sTN58, CD44 Ab and nuclei are visualized in red, green, and blue, respectively. Magnification 63×, 1.0× digital zoom, scale bar = 10 μm. Co-localization results appear yellow in the merged images (Overlap Coefficient 0.74). All digital images were captured under identical settings to allow direct comparison of staining patterns. (C) Flow cytometry analyses of Cis-Pt-R, MDA-MB-231, BT-549 and BT-474 cells treated with CD44-PE Ab or Alexa 647-sTN58. (D) Quantification of the geometric mean fluorescence intensity (gMFI) of Alexa 647-sTN58- or CD44-PE Ab-treated cells normalized to the gMFI of the untreated cells. Bars depict mean ± SD of at least two independent experiments. ∗∗∗ P < 0.001, ∗∗∗∗ P < 0.0001 relative to untreated cells; ns, no significant.

Article Snippet: For cell binding of anti-CD44 antibody, 2.0 × 10 5 cells were left untreated or incubated for 20 min at RT with CD44 phycoerythrin (PE)-conjugated antibody (CD44-PE Ab, IM7, 0.25 μg/test, Santa Cruz Biotechnology) in DPBS supplemented with 0.1 % bovine serum albumin.

Techniques: Incubation, Staining, Confocal Microscopy, Negative Control, Comparison, Flow Cytometry, Fluorescence

Journal: Bioactive Materials

Article Title: A novel CD44-targeting aptamer recognizes chemoresistant mesenchymal stem-like TNBC cells and inhibits tumor growth

doi: 10.1016/j.bioactmat.2025.04.027

Figure Lengend Snippet: CD44 silencing results in reduced sTN58 binding. (A, E) Cis-Pt-R (A) and BT-549 (E) cells were left untreated or transfected with si-CD44 or siRNA ctrl. At 48 h post-transfection, cells were harvested, and cell lysates prepared and immunoblotted with CD44 Ab. Equal loading was confirmed by immunoblot with anti-α-tubulin antibody. Molecular weights of protein markers are reported. (B, F) The histogram depicts the densitometric ratio of CD44 expression to α-tubulin. Values are shown relative to the untreated control, arbitrarily set to 1. ∗ P < 0.05, ∗∗ P < 0.01 relative to siRNA ctrl. (C, G) Binding of CD44-PE Ab ( left ) and Alexa 647-sTN58 ( right ) to Cis-Pt-R (C) and BT-549 (G) cells following 48 h transfection with si-CD44 (green) and siRNA ctrl (gray). (D, H) The histogram shows gMFI of si-CD44-transfected cells treated with sTN58 aptamer or CD44 Ab, normalized to the gMFI of untreated cells, and expressed as percentage with respect to siRNA ctrl-transfected cells. ∗∗∗∗ P < 0.0001 relative to siRNA ctrl. (I) Immunoblot analysis of CD44 and the housekeeping protein α-tubulin. The molecular weights of protein markers are reported. (J) The histogram shows the relative fold-change in CD44 expression levels compared to α-tubulin, normalized to MDA-MB-231 target cells, whose expression level is arbitrarily set to 1. ∗ P < 0.05, ∗∗∗ P < 0.001 relative to MDA-MB-231. (K) Flow cytometry analyses of Cis-Pt-R, MCF 10A, THP-1 and HS-5 cells treated with Alexa 647-sTN58. (L) Quantification of the gMFI of Alexa 647-sTN58-treated cells normalized to the gMFI of the untreated cells. ∗∗ P < 0.01, ∗∗∗∗ P < 0.0001 relative to untreated cells; ns, no significant. In B, D, F, H, J, L, bars depict mean ± SD of at least two independent experiments.

Article Snippet: For cell binding of anti-CD44 antibody, 2.0 × 10 5 cells were left untreated or incubated for 20 min at RT with CD44 phycoerythrin (PE)-conjugated antibody (CD44-PE Ab, IM7, 0.25 μg/test, Santa Cruz Biotechnology) in DPBS supplemented with 0.1 % bovine serum albumin.

Techniques: Binding Assay, Transfection, Western Blot, Expressing, Control, Flow Cytometry

Journal: Bioactive Materials

Article Title: A novel CD44-targeting aptamer recognizes chemoresistant mesenchymal stem-like TNBC cells and inhibits tumor growth

doi: 10.1016/j.bioactmat.2025.04.027

Figure Lengend Snippet: sTN58 aptamer and CD44 Ab colocalize with integrin β1 Ab on Cis-Pt-R cells. (A) Following 5 min incubation at RT with 2 μM Alexa 647-sTN58, Cis-Pt-R cells were stained with integrin β1 Ab, visualized by confocal microscopy, and photographed. (B) Cell lysates from Cis-Pt-R cells left untreated or treated for 48 h with 100 nM siRNA ctrl or si-ITGB1 were analyzed by immunoblotting with integrin β1, CD44 and anti-α-tubulin antibodies. Molecular weights of protein markers are reported. (C) The histogram shows the protein expression/α-tubulin ratio based on the densitometric signals. Values are shown relative to untreated samples, arbitrarily set to 1. (D) Binding of integrin β1-APC-Cy7 Ab ( left ) and Alexa 647-sTN58 ( right ) to Cis-Pt-R cells following 48 h transfection with siRNA ctrl (gray) and si-ITGB1 (pink). (E) The histogram shows gMFI of si-ITGB1-transfected cells treated with Alexa 647-sTN58 or integrin β1-APC-Cy7 Ab, normalized to the gMFI of untreated cells, and expressed as percentage with respect to siRNA ctrl-transfected cells. Bars depict mean ± SD of two independent experiments. ∗∗∗ P < 0.001; ns, no significant. (F) Confocal microscopy analyses of A431 cells treated with sTN58 and stained with integrin β1 Ab, as in A, or stained with CD44-PE and integrin β1 antibodies. Alexa 647-SCR was used as a negative control. In A, F, aptamers and CD44-PE Ab are visualized in red, integrin β1 Ab in green and nuclei in blue. All digital images were captured at the same setting to allow direct comparison of staining patterns. Magnification 63×, 1.0× digital zoom, scale bar = 10 μm. Co-localization results appear yellow in the merged images. Arrowheads indicate some co-localization points between sTN58 and integrin β1 Ab (Overlap Coefficient, 0.80). (G) Flow cytometry analyses of A431 cells treated with CD44-PE Ab, Alexa 647-sTN58 and integrin β1-APC-Cy7 Ab. (H) Quantification of the gMFI of sTN58-, CD44 PE- and integrin β1-APC-Cy7-treated cells normalized to the gMFI of the untreated cells. Bars depict mean ± SD of three independent experiments. ∗∗∗∗ P < 0.0001 relative to untreated cells; ns, no significant.

Article Snippet: For cell binding of anti-CD44 antibody, 2.0 × 10 5 cells were left untreated or incubated for 20 min at RT with CD44 phycoerythrin (PE)-conjugated antibody (CD44-PE Ab, IM7, 0.25 μg/test, Santa Cruz Biotechnology) in DPBS supplemented with 0.1 % bovine serum albumin.

Techniques: Incubation, Staining, Confocal Microscopy, Western Blot, Expressing, Binding Assay, Transfection, Negative Control, Comparison, Flow Cytometry

Journal: Bioactive Materials

Article Title: A novel CD44-targeting aptamer recognizes chemoresistant mesenchymal stem-like TNBC cells and inhibits tumor growth

doi: 10.1016/j.bioactmat.2025.04.027

Figure Lengend Snippet: sTN58 inhibits invasive growth and vessel like-structures formation in 3D cell cultures. (A) Representative phase-contrast images of Cis-Pt-R cells grown in 2D or in Matrigel (3D) in the presence of 500 nM sTN58 or SCR for the indicated time points. (B) The invasive ability of Cis-Pt-R cells at 5 days is expressed as the number of colonies and branches per field. (C, D) Invasion of Cis-Pt-R (C) and Dox-R (D) cells toward 10 % FBS was analyzed by transwell invasion assay in the presence of 500 nM sTN58 or SCR for 72 h. Photographs of a representative experiment are shown. (E, F) Data are presented as percentage of invaded cells in the presence of sTN58 compared with SCR control. (G, I) Representative phase-contrast images of Cis-Pt-R cells (G) and Dox-R (I) grown on Matrigel in the presence of HA and treated with 500 nM sTN58 or SCR for 24 h. (H, J) Tube formation ability is expressed as the number of junctions and loops per field. (A, C, D, G, I) Magnification 10×, scale bar = 200 μm. (B, E, F, H, J) Bars depict means ± SEM of at least two independent experiments. ∗∗ P < 0.01, ∗∗∗ P < 0.001, ∗∗∗∗ P < 0.0001 relative to SCR-treated cells. (K) AF3 molecular docking model of sTN58-CD44 binding complex; sTN58, HA-binding site and CD44 folded domain are shown in blue, white and green, respectively.

Article Snippet: For cell binding of anti-CD44 antibody, 2.0 × 10 5 cells were left untreated or incubated for 20 min at RT with CD44 phycoerythrin (PE)-conjugated antibody (CD44-PE Ab, IM7, 0.25 μg/test, Santa Cruz Biotechnology) in DPBS supplemented with 0.1 % bovine serum albumin.

Techniques: Transwell Invasion Assay, Control, Binding Assay

Journal: Bioactive Materials

Article Title: A novel CD44-targeting aptamer recognizes chemoresistant mesenchymal stem-like TNBC cells and inhibits tumor growth

doi: 10.1016/j.bioactmat.2025.04.027

Figure Lengend Snippet: sTN58 selectively targets CD44-positive 4T1 xenografts. (A) Representative confocal images of 4T1 (8.0 × 10 4 cells) incubated with 2 μM Alexa 647-sTN58 or Alexa 647-SCR and then fixed and stained with CD44 Ab. Aptamers, CD44 Ab and nuclei are visualized in red, green and blue, respectively. Co-localization results appear yellow in the merged images (Overlap Coefficient, 0.76). All digital images were captured at the same setting to allow direct comparison of staining patterns. Magnification 63× , 1.0× digital zoom, scale bar = 10 μm. (B) Binding of CD44-PE Ab ( left ) and Alexa 647-sTN58 ( right ) to 4T1 cells using flow cytometry. (C) Quantification of the gMFI of sTN58 aptamer- or CD44 Ab-treated cells normalized to the gMFI of the untreated cells. Bars depict mean ± SD of two independent experiments. ∗∗ P < 0.01, ∗∗∗ P < 0.001 relative to untreated cells. (D) Mice bearing mammary fat pad orthotopic 4T1 tumors were i.v. injected with 0.75 nmol of either NIR-sTN58 or NIR-SCR and analyzed with FMT at the indicated time points; Pre, before injection. Representative volume renderings taken at the same color gating for NIR-sTN58 and NIR-SCR injected mice are shown. (E) The amount of fluorescence (pmol) was quantified in specific VOIs encompassing the tumor in the animal. (F) Representative ex vivo FRI imaging of tumor and major organs (liver, kidneys, spleen, lung, heart and muscle) harvested from mice at 24 h post-injection of NIR-sTN58 and NIR-SCR. (G) The histogram indicates the mean FRI Signal Intensity of tumors and organs in the two groups. (E, G) Bars depict mean ± SD. ∗∗ P < 0.01; ∗∗∗ P < 0.001 relative to NIR-SCR; ns, no significant. (H) Plasma pharmacokinetic profile of sTN58. Concentration of aptamer is shown as a function of time following a single i.v. injection in Balb/c mice. Data are presented as the mean ± SEM.

Article Snippet: For cell binding of anti-CD44 antibody, 2.0 × 10 5 cells were left untreated or incubated for 20 min at RT with CD44 phycoerythrin (PE)-conjugated antibody (CD44-PE Ab, IM7, 0.25 μg/test, Santa Cruz Biotechnology) in DPBS supplemented with 0.1 % bovine serum albumin.

Techniques: Incubation, Staining, Comparison, Binding Assay, Flow Cytometry, Injection, Fluorescence, Ex Vivo, Imaging, Clinical Proteomics, Concentration Assay

Journal: Science Advances

Article Title: Gene regulatory network topology governs resistance and treatment escape in glioma stem-like cells

doi: 10.1126/sciadv.adj7706

Figure Lengend Snippet: UMAP plots of scRNA-seq profiles, annotated according to treatment conditions (untreated control, vehicle—DMSO, and pitavastatin—PSTAT), for ( A ) SN520 and ( B ) SN503. Scatterplots show proportions of each subtype in each PD-GSC population across treatment for ( C ) SN520 and ( D ) SN503. ( E and F ) Flow cytometry analysis of PN and MES markers CD133 (PN) and CD44 (MES) across pitavastatin-treated cells for SN520 and SN503, respectively. Values (gray) indicate percentages of cell populations in each quadrant. Proportions of cells positive for each subtype marker are quantified in the adjacent bar plots underneath. ( G and H ) Heatmap of inferCNV scores for SN520 and SN503, respectively. Cells (rows) are grouped based on treatment conditions [same color annotation as in (A) and (B)]. Genes (columns) are arranged according to their chromosomal positions. ( I ) Dose-response curves of naïve SN520 PD-GSCs (light blue) and SN520 PD-GSCs that survived an initial pitavastatin treatment (treated—dark blue). Adjacent plot shows corresponding area under the curve (AUC) values from dose-response curves generated from subsequent PD-GSC cultures derived from original pitavastatin or vehicle control treatment for SN520 (left) and SN503 (right). Paired t test results showed a sustained (significant) increase in AUC values of the PSTAT-treated SN520 PD-GSCs relative to their vehicle control counterparts but not for SN503.

Article Snippet: An anti-Hu CD44 antibody conjugated with phycoerythrin (PE) (eBioscience) and an anti-Hu/Mo CD133 antibody conjugated with fluorescein isothiocyanate (FITC) (eBioscience) were used to assess expression of these two surface proteins across each PD-GSC population.

Techniques: Control, Flow Cytometry, Marker, Generated, Derivative Assay