Journal: International Journal of Oncology

Article Title: lnc-PKD2-2-3, identified by long non-coding RNA expression profiling, is associated with pejorative tumor features and poor prognosis, enhances cancer stemness and may serve as cancer stem-cell marker in cholangiocarcinoma

doi: 10.3892/ijo.2019.4798

Figure Lengend Snippet: Primers used for quantitative PCR.

Article Snippet: The antibodies used in flow cytometry were CD133 mouse monoclonal antibody (cat. no. 38725, flow-specific; Alexa Fluor ® 488-conjugated; Cell Signaling Technology, Inc.) and CD44 rat monoclonal antibody (cat. no. 80813; allophycocyanin-conjugated; Cell Signaling Technology, Inc.).

Techniques:

Journal: International Journal of Oncology

Article Title: lnc-PKD2-2-3, identified by long non-coding RNA expression profiling, is associated with pejorative tumor features and poor prognosis, enhances cancer stemness and may serve as cancer stem-cell marker in cholangiocarcinoma

doi: 10.3892/ijo.2019.4798

Figure Lengend Snippet: Antibodies used for western blotting.

Article Snippet: The antibodies used in flow cytometry were CD133 mouse monoclonal antibody (cat. no. 38725, flow-specific; Alexa Fluor ® 488-conjugated; Cell Signaling Technology, Inc.) and CD44 rat monoclonal antibody (cat. no. 80813; allophycocyanin-conjugated; Cell Signaling Technology, Inc.).

Techniques: Western Blot

Journal: International Journal of Oncology

Article Title: lnc-PKD2-2-3, identified by long non-coding RNA expression profiling, is associated with pejorative tumor features and poor prognosis, enhances cancer stemness and may serve as cancer stem-cell marker in cholangiocarcinoma

doi: 10.3892/ijo.2019.4798

Figure Lengend Snippet: Correlation of lnc-PKD2-2-3 with CSC marker expression. Lnc-PKD2-2-3 expression was positively associated with (A) CD44, (B) CD133 and (C) OCT4 expression in cholangiocarcinoma tumor tissues. Correlation was determined by Spearman test. CSC, cancer stem cell; OCT4, octamer-binding transcription factor 4.

Article Snippet: The antibodies used in flow cytometry were CD133 mouse monoclonal antibody (cat. no. 38725, flow-specific; Alexa Fluor ® 488-conjugated; Cell Signaling Technology, Inc.) and CD44 rat monoclonal antibody (cat. no. 80813; allophycocyanin-conjugated; Cell Signaling Technology, Inc.).

Techniques: Marker, Expressing, Binding Assay

Journal: International Journal of Oncology

Article Title: lnc-PKD2-2-3, identified by long non-coding RNA expression profiling, is associated with pejorative tumor features and poor prognosis, enhances cancer stemness and may serve as cancer stem-cell marker in cholangiocarcinoma

doi: 10.3892/ijo.2019.4798

Figure Lengend Snippet: CSC marker expression and CD44 + CD133 + cell proportion following lentivirus transduction. (A) mRNA expression levels of CD44, (B) CD133 and (C) OCT4 in TFK-1 experimental cell groups. (D) Representative western blot of CSC marker expression in TFK-1 experimental cell groups. (E) Quantification and (F) representative plots of flow cytometry analysis for CD44 + CD133 + proportions in TFK-1 experimental cell groups. (G) mRNA expression levels of CD44, (H) CD133 and (I) OCT4 in Huh-28 experimental cell groups. (J) Representative western blot of CSC marker expression in Huh-28 experimental cell groups. (K) Quantification and (L) representative plots of flow cytometry analysis for CD44 + CD133 + proportions in Huh-28 experimental cell groups. * P<0.05, ** P<0.01 and *** P<0.001, with comparisons indicated by brackets. CSC, cancer stem cell; NC, negative control.

Article Snippet: The antibodies used in flow cytometry were CD133 mouse monoclonal antibody (cat. no. 38725, flow-specific; Alexa Fluor ® 488-conjugated; Cell Signaling Technology, Inc.) and CD44 rat monoclonal antibody (cat. no. 80813; allophycocyanin-conjugated; Cell Signaling Technology, Inc.).

Techniques: Marker, Expressing, Transduction, Western Blot, Flow Cytometry, Negative Control

Journal: International Journal of Oncology

Article Title: lnc-PKD2-2-3, identified by long non-coding RNA expression profiling, is associated with pejorative tumor features and poor prognosis, enhances cancer stemness and may serve as cancer stem-cell marker in cholangiocarcinoma

doi: 10.3892/ijo.2019.4798

Figure Lengend Snippet: Validation of cholangiocarcinoma stem-like cells and lnc-PKD2-2-3 expression. (A) mRNA levels of CD44, (B) CD133 and (C) OCT4, as well as (D) their protein levels were measured in the S-TFK-1 and parental TFK-1 cells. (E) Lnc-PKD2-2-3 levels in the S-TFK-1 and parental TFK-1 cells. (F) mRNA levels of CD44, (G) CD133 and (H) OCT4, as well as (I) their protein levels were measured in the S-Huh-28 and parental Huh-28 cells. (J) Lnc-PKD2-2-3 levels in the S-Huh-28and parental Huh-28 cells. ** P<0.01 and *** P<0.001, with comparisons indicated by brackets. S, stem-like; OCT4, octamer-binding transcription factor 4.

Article Snippet: The antibodies used in flow cytometry were CD133 mouse monoclonal antibody (cat. no. 38725, flow-specific; Alexa Fluor ® 488-conjugated; Cell Signaling Technology, Inc.) and CD44 rat monoclonal antibody (cat. no. 80813; allophycocyanin-conjugated; Cell Signaling Technology, Inc.).

Techniques: Biomarker Discovery, Expressing, Binding Assay

Journal: Translational Oncology

Article Title: Photoimmunotheranostics of epithelioid sarcoma by targeting CD44 or EGFR

doi: 10.1016/j.tranon.2024.101966

Figure Lengend Snippet: CD44 and EGFR overexpression in VA-ES-BJ cells and in human ES. (a) The cell surface expression of CD44 and EGFR on VA-ES-BJ cells measured by flow cytometry. The corresponding isotype antibodies were used as controls. (b) Representative images from three VA-ES-BJ xenograft tumor sections after H&E staining (left), immunostaining for CD44 (middle) or EGFR (right) at 20× magnification. Scale bar = 100 μm. Representative images from human ES tumor tissue sections after H&E staining (c), immunostaining for CD44 (d) and EGFR (e) at 20× magnification. Human ES tumor tissue samples were resected from four ES patients. Scale bar = 100 μm.

Article Snippet: An anti-CD44 monoclonal mouse antibody (clone 8E2, Cell Signaling) and an anti-EGFR monoclonal rat antibody (clone D38B1, Cell Signaling) were used to probe CD44 and EGFR, respectively.

Techniques: Over Expression, Expressing, Flow Cytometry, Staining, Immunostaining

Journal: Translational Oncology

Article Title: Photoimmunotheranostics of epithelioid sarcoma by targeting CD44 or EGFR

doi: 10.1016/j.tranon.2024.101966

Figure Lengend Snippet: Concentration and exposure-dependence and target-specific cell death of CD44-IR700 and EGFR-IR700. CD44-IR700-mediated phototoxicity was dependent on the concentration of CD44-IR700 (a) or exposure dose (b). (c) CD44-specific cell death only occurred when VA-ES-BJ cells were exposed to CD44-IR700 and light irradiation. EGFR-IR700-mediated phototoxicity was dependent on the concentration of EGFR-IR700 (d) or exposure dose (e). (f) EGFR-specific cell death only occurred when VA-ES-BJ cells were exposed to both EGFR-IR700 and light irradiation.

Article Snippet: An anti-CD44 monoclonal mouse antibody (clone 8E2, Cell Signaling) and an anti-EGFR monoclonal rat antibody (clone D38B1, Cell Signaling) were used to probe CD44 and EGFR, respectively.

Techniques: Concentration Assay, Irradiation

Journal: Translational Oncology

Article Title: Photoimmunotheranostics of epithelioid sarcoma by targeting CD44 or EGFR

doi: 10.1016/j.tranon.2024.101966

Figure Lengend Snippet: Preferential accumulation of CD44-IR700 or EGFR-IR700 in VA-ES-BJ tumors. NIR fluorescence imaging of nude mice bearing bilateral VA-ES-BJ tumors over a 24-h period. 100 μg of CD44-IR700 (a) or EGFR-IR700 (b) or IgG-IR700 (c) antibody conjugate was injected i.v. (d) Plots of tumor to normal (T/N) ratios measured at 0 min, 1 h, 6 h and 24 h p.i. ROIs of tumors and normal tissue were drawn on in vivo NIR fluorescence images. T/N ratios were derived from the MFI of ROIs and represented as Mean ± SD for all three groups ( n = 10 per group). Comparisons of T/N ratios between the groups at 6 h p.i. and 24 h p.i. are shown on the right, ns: no significance, * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. (e) Ex vivo fluorescence images of whole tumors resected at 24 h p.i. (f) The MFI of resected tumors at 24 h p.i. in different groups. Values represent Mean ± SD from six tumors per group ( n = 6). (g) Bio-distribution of antibody conjugates in main organs and tumors resected at 24 h p.i. H, heart; Li, liver; Sp, spleen; Lu, lung; K, kidney; In, intestine; St, stomach; Mu, muscle; Bn, bone; Bl, blood; T, tumor. Values (Mean ± SD) are normalized to % injected dose/g (% ID /g) from three mice per group ( n = 3). Only comparisons with p value less than 0.05 displayed, * P < 0.05, *** P < 0.001, **** P < 0.0001.

Article Snippet: An anti-CD44 monoclonal mouse antibody (clone 8E2, Cell Signaling) and an anti-EGFR monoclonal rat antibody (clone D38B1, Cell Signaling) were used to probe CD44 and EGFR, respectively.

Techniques: Fluorescence, Imaging, Injection, In Vivo, Derivative Assay, Ex Vivo

Journal: Translational Oncology

Article Title: Photoimmunotheranostics of epithelioid sarcoma by targeting CD44 or EGFR

doi: 10.1016/j.tranon.2024.101966

Figure Lengend Snippet: In vivo CD44-IR700 or EGFR-IR700-PIT. (a) Growth curve of VA-ES-BJ tumors. 100 μg of CD44-IR700 or EGFR-IR700 or IgG-IR700 was injected i.v. on day 0 and on day 7. All the groups were monitored for three weeks after injection except for two weeks in PBS group. PIT groups received light exposure at 200 J/cm 2 , 24 h after each injection (pointed by blue arrows) and mice in the no PIT groups were shielded from light. Values represent Mean ± SEM from at least four mice per group ( n ≥ 4). (b) The comparisons of tumor volumes between the groups at each monitoring point, ns: no significance, * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. (c) Photographs of representative VA-ES-BJ tumors harvested at the end of treatment.

Article Snippet: An anti-CD44 monoclonal mouse antibody (clone 8E2, Cell Signaling) and an anti-EGFR monoclonal rat antibody (clone D38B1, Cell Signaling) were used to probe CD44 and EGFR, respectively.

Techniques: In Vivo, Injection

Journal: Translational Oncology

Article Title: Photoimmunotheranostics of epithelioid sarcoma by targeting CD44 or EGFR

doi: 10.1016/j.tranon.2024.101966

Figure Lengend Snippet: Short-term effects of PIT on CD44 and EGFR. (a) Immunoblots probing CD44 and EGFR protein in VA-ES-BJ tumors. (b) Representative flow cytometry profiles of CD44 and EGFR expression in tumors after receiving PITs. 100 μg of CD44-IR700 or EGFR-IR700 or 100 μl of PBS was injected i.v. PIT groups received light exposure at 200 J/cm 2 24 h after injection and mice in the PBS group were shielded from light. VA-ES-BJ tumors were harvested three days after single PIT. Tumors were dissociated into a single cell suspension and only live cells were included in the flow cytometry analysis.

Article Snippet: An anti-CD44 monoclonal mouse antibody (clone 8E2, Cell Signaling) and an anti-EGFR monoclonal rat antibody (clone D38B1, Cell Signaling) were used to probe CD44 and EGFR, respectively.

Techniques: Western Blot, Flow Cytometry, Expressing, Injection, Suspension

Journal: bioRxiv

Article Title: Super-enhancer profiling reveals ThPOK/ZBTB7B, a CD4 + cell lineage commitment factor, as a master regulator that restricts breast cancer cells to a luminal non-migratory phenotype

doi: 10.1101/2024.09.21.614267

Figure Lengend Snippet: a, b, d-f, h-i) Gene expression levels measured by qRT-PCR. Since three different shRNA against ThPOK were used, the circle for each gene is divided in thirds, one for each shRNA. The color of each third indicates the log 2 (fold-change) and the size the -log 10 (p-value), for a t -test relative to the control shRNA (shScr). Each gene was assessed in ≥3 biological replicates. Differential expression is shown in color scale as a log2 of the fold change, and p-values by the size of the circle as –log10. c) Morphological changes associated with ThPOK deficiency in Luminal and HER2+ cells (10X) magnification. Scale: each side of the square is 400µm. g) Flow cytometry analysis showing CD44 expression in Luminal and HER2+ scramble (Scr) and ThPOK-kd cells. j-k) Migration assays. j) Scratch assay showing increased migratory features of ThPOK-kd cells compared with control (scr) cells. Error bars represent the SD of ≥3 biological replicates. T47D cells p=4.07×10 −19 , MCF7 cells p=8.087×10 −8 . k) Boyden chamber assay. Error bars represent the SD of ≥3 biological replicates, p *<0.05, **<10 −4 .

Article Snippet: Cells were stained for 1 hour with an anti-CD44-PE antibody (Cell Signaling, cat# 88151) at a 1:300 dilution in FACS buffer.

Techniques: Gene Expression, Quantitative RT-PCR, shRNA, Control, Quantitative Proteomics, Flow Cytometry, Expressing, Migration, Wound Healing Assay, Boyden Chamber Assay