Journal: Cancer Biology & Therapy

Article Title: Combination therapy of niclosamide with gemcitabine inhibited cell proliferation and apoptosis via Wnt/β-catenin/c-Myc signaling pathway by inducing β-catenin ubiquitination in pancreatic cancer

doi: 10.1080/15384047.2023.2272334

Figure Lengend Snippet: Niclosamide decreases cell proliferation and inhibits linear ubiquitination of β-catenin.

Article Snippet: Primary antibodies rabbit monoclonal anti-phospho-β-catenin (S33/37/T41), anti-β-catenin, anti-GSK3β, anti-β-TrCP (1:100, Cell Signaling Technology, Danvers, MA, USA) were added and incubated at 4°C overnight.

Techniques:

Journal: Cancers

Article Title: TIM-3 Expression and M2 Polarization of Macrophages in the TGFβ-Activated Tumor Microenvironment in Colorectal Cancer

doi: 10.3390/cancers15204943

Figure Lengend Snippet: Association of TGFB with HAVCR2 , M2 macrophage signature and TGFβ-stromal signature (TBSS) in multiple RNA-seq or microarray cohorts of CRC in conjunction with MSI status and CMS subtypes. ( A , B ) Correlations between the expression of TGFB and HAVCR2 in MSI ( A ) and MSS ( B ) CRC. Spearman’s coefficients are indicated ( p < 0.0001). ( C ) HAVCR2 expression in MSI and MSS CRC. ( D ) Volcano plot displaying differentially expressed genes between TBSS Low and TBSS High tumors. The x-axis shows the log 2 -fold change, and the y-axis displays the -log 10 of the p -values. ( E ) Correlations of TGFB with HAVCR2 (red), M2 macrophage (yellow) and TBSS (green) in six independent cohorts of CRC. Spearman’s coefficients are shown as colors corresponding to HAVCR2 (red), M2 macrophage (yellow) and TBSS (green) for each dataset. p -values for all correlations < 0.0001.

Article Snippet: Slides were incubated with primary rabbit polyclonal anti-VCAN antibody (HPA004726, Prestige Antibodies ® Powered by Atlas Antibodies, Sigma-Aldrich, St Louis, MO, USA; 1:500) or primary rabbit monoclonal anti-TIM-3 antibody (D5D5R XP ® ; #45208; Cell Signaling Technology, Danvers, MA, USA; 1:400) at 4 °C overnight, and then detected using a horseradish peroxidase-coupled anti-rabbit polymer (K4003; Envision+ system, Agilent Technologies).

Techniques: RNA Sequencing Assay, Microarray, Expressing

Journal: Cancers

Article Title: TIM-3 Expression and M2 Polarization of Macrophages in the TGFβ-Activated Tumor Microenvironment in Colorectal Cancer

doi: 10.3390/cancers15204943

Figure Lengend Snippet: Association between CMS subtypes and the levels of TGFB , TGFβ-stromal signature (TBSS), M2 macrophage signature and HAVCR2 expression in six independent cohorts of CRC, including TCGA, GSE39582, GSE33113, GSE14333, GSE37892 and KFSYSCC. MSI status was available for the former three cohorts; red dots represent MSI tumors. Kruskal-Wallis test, followed by Dunn’s post hoc test to compare each CMS subtype with CMS2. **** p < 0.0001, *** p < 0.001, ** p < 0.01, * p < 0.05, ns p > 0.05.

Article Snippet: Slides were incubated with primary rabbit polyclonal anti-VCAN antibody (HPA004726, Prestige Antibodies ® Powered by Atlas Antibodies, Sigma-Aldrich, St Louis, MO, USA; 1:500) or primary rabbit monoclonal anti-TIM-3 antibody (D5D5R XP ® ; #45208; Cell Signaling Technology, Danvers, MA, USA; 1:400) at 4 °C overnight, and then detected using a horseradish peroxidase-coupled anti-rabbit polymer (K4003; Envision+ system, Agilent Technologies).

Techniques: Expressing

Journal: Cancers

Article Title: TIM-3 Expression and M2 Polarization of Macrophages in the TGFβ-Activated Tumor Microenvironment in Colorectal Cancer

doi: 10.3390/cancers15204943

Figure Lengend Snippet: Stroma-specific association of TGFB with TGFβ-stromal signature (TBSS), M2 macrophage signature and HAVCR2 . ( A – C ) Primary CRC tissues (orange) and matched organoids (purple) in an RNA-seq dataset (GSE171682). ( D – F ) CRC tissues (orange), organoids (purple), xenografts (blue) and cell lines (black) in a microarray dataset (GSE100550). Spearman’s coefficients are indicated as colored numbers corresponding to tissues (orange), organoids (purple), xenografts (blue) and cell lines (black) for each dataset.

Article Snippet: Slides were incubated with primary rabbit polyclonal anti-VCAN antibody (HPA004726, Prestige Antibodies ® Powered by Atlas Antibodies, Sigma-Aldrich, St Louis, MO, USA; 1:500) or primary rabbit monoclonal anti-TIM-3 antibody (D5D5R XP ® ; #45208; Cell Signaling Technology, Danvers, MA, USA; 1:400) at 4 °C overnight, and then detected using a horseradish peroxidase-coupled anti-rabbit polymer (K4003; Envision+ system, Agilent Technologies).

Techniques: RNA Sequencing Assay, Microarray

Journal: Cancers

Article Title: TIM-3 Expression and M2 Polarization of Macrophages in the TGFβ-Activated Tumor Microenvironment in Colorectal Cancer

doi: 10.3390/cancers15204943

Figure Lengend Snippet: Immunohistochemistry for a TGFβ-responsive stromal protein, VCAN ( A , B ), and TIM-3 + tumor-infiltrating immune cells (TIICs) ( C – F ) in CRC tissues. ( A , C , E ) Serial sections from a representative case of CRC showing negative stromal VCAN staining ( A ) with low infiltration of TIM-3 + TIICs ( C , E ). ( B , D , F ) Serial sections from a representative case of CRC showing strong stromal VCAN staining ( B ) with dense TIM-3 + TIICs ( D , F ). ( G ) Representative immunofluorescence of CD163 (green), TIM-3 (red) and DAPI (blue) in CRC tissues. Scale bar, 100μm. ( H ) Association between the levels of TIM-3 + TIICs and stromal VCAN in CRC ( n = 45) by Spearman’s correlation. ( I ) Association between TIM-3 + TIICs and heterogenous VCAN expression patterns (VCAN Low areas and VCAN High areas) within the tumor ( n = 24). Pairwise significance was tested using the Wilcoxon signed rank test.

Article Snippet: Slides were incubated with primary rabbit polyclonal anti-VCAN antibody (HPA004726, Prestige Antibodies ® Powered by Atlas Antibodies, Sigma-Aldrich, St Louis, MO, USA; 1:500) or primary rabbit monoclonal anti-TIM-3 antibody (D5D5R XP ® ; #45208; Cell Signaling Technology, Danvers, MA, USA; 1:400) at 4 °C overnight, and then detected using a horseradish peroxidase-coupled anti-rabbit polymer (K4003; Envision+ system, Agilent Technologies).

Techniques: Immunohistochemistry, Staining, Immunofluorescence, Expressing

Journal: Cancers

Article Title: TIM-3 Expression and M2 Polarization of Macrophages in the TGFβ-Activated Tumor Microenvironment in Colorectal Cancer

doi: 10.3390/cancers15204943

Figure Lengend Snippet: TIM-3 expression on M2 and M1-polarized macrophages and TGFβ-treated monocytes. ( A , B ) TIM-3 expression on M0 and M2-polarized macrophages. Representative histograms for TIM-3 are shown ( A ), and the expression levels of TIM-3 on M2 macrophages present as the mean ± s.e.m. relative to those of M0 macrophages ( n = 4) ( B ). Mann–Whitney U test. * p < 0.05. ( C , D ) TIM-3 expression on M0 and M1-polarized macrophages. Representative histograms for TIM-3 ( C ), and the levels of TIM-3 on M1 macrophages as the mean ± s.e.m. relative to those of M0 macrophages ( n = 3) ( D ). n.s. p > 0.05. ( E , F ) Representative histograms displaying TIM-3 expression on monocytes treated with various concentrations of TGFβ ( E ), and TIM-3 expression levels on TGFβ-treated monocytes present as the mean ± s.e.m. relative to those of controls ( n = 10) ( F ). Kruskal-Wallis test with Dunn’s post hoc test. *** p < 0.001.

Article Snippet: Slides were incubated with primary rabbit polyclonal anti-VCAN antibody (HPA004726, Prestige Antibodies ® Powered by Atlas Antibodies, Sigma-Aldrich, St Louis, MO, USA; 1:500) or primary rabbit monoclonal anti-TIM-3 antibody (D5D5R XP ® ; #45208; Cell Signaling Technology, Danvers, MA, USA; 1:400) at 4 °C overnight, and then detected using a horseradish peroxidase-coupled anti-rabbit polymer (K4003; Envision+ system, Agilent Technologies).

Techniques: Expressing, MANN-WHITNEY

Journal: bioRxiv

Article Title: Inhibition of Asparagine Synthetase Effectively Retards Polycystic Kidney Disease Progression

doi: 10.1101/2023.10.10.561720

Figure Lengend Snippet: A. Schematic representation CAD-dependent de novo pyrimidine biosynthesis pathway and targeted metabolomic profile of relative intermediates normalized on protein content, of P160 Tam-Cre;Pkd1 ΔC/flox cystic and control kidneys treated with ASOs. B. Quantification of Ki67 positive nuclei in the epithelium lining the cysts in kidney cortex of Tam-Cre;Pkd1 ΔC/flox mice at P94, treated with Scr- or Asns -ASO. Data information: In A data are shown as mean ± SD. One-way ANOVA, corrected with Tukey’s multiple comparisons. In B data are shown as mean ± SD. Student’s unpaired two-tailed t-test. ns non- significant; *p<0.05; **p<0.01; ***p<0.001.

Article Snippet: Primary antibody against Ki-67 ((D3B5) Rabbit mAb (Mouse Preferred; IHC Formulated) (CST, #12202)) was used 1:200 and developed with Bond Polymer Refine Detection (Leica, DS9800).

Techniques: Two Tailed Test

Journal: iScience

Article Title: Pigmented skin exhibits accelerated wound healing compared to the nonpigmented skin in Guinea pig model

doi: 10.1016/j.isci.2023.108159

Figure Lengend Snippet:

Article Snippet: Rabbit monoclonal Vimentin primary antibody , Cell Signaling Technology , Cat no.# 5741; RRID: AB_10695459.

Techniques: Recombinant, SYBR Green Assay, Modification, Purification, Enzyme-linked Immunosorbent Assay, Software

Journal: bioRxiv

Article Title: Short N-terminal disordered regions and the proline-rich domain are major regulators of phase transitions for full-length UBQLN1, UBQLN2 and UBQLN4

doi: 10.1101/2023.09.27.559790

Figure Lengend Snippet: (A) Domain architectures of UBQLN1, UBQLN2 and UBQLN4. The proline-rich repeat (Pxx) region is unique to UBQLN2. (B) Brightfield microscopy shows 200 µM solutions of the three proteins in buffer containing 20 mM NaPhosphate, 200 mM NaCl, 0.5 mM TCEP, and EDTA (pH 6.8) after incubation at 30 °C for 5 minutes. Imaging was done at the coverslip. Scale bar, 10 µm. (C) Phase diagrams determined from c sat measurements as a function of temperature. Phase separation is observed above these coexistence lines. Error bars represent SD over at least four trials from two different proteins preps.

Article Snippet: Primary antibodies include UBQLN2 rabbit mAb (Cell Signaling Technology 85509), rabbit UBQLN2 pAb (Proteintech 23449-1-AP) or UBQLN2 mouse mAb (Novus Biologicals NBP2-25164).

Techniques: Microscopy, Incubation, Imaging

Journal: bioRxiv

Article Title: Short N-terminal disordered regions and the proline-rich domain are major regulators of phase transitions for full-length UBQLN1, UBQLN2 and UBQLN4

doi: 10.1101/2023.09.27.559790

Figure Lengend Snippet: Phase diagrams for (A) UBQLN2 and UBQLN4 as well as UBQLN2 without its unique Pxx region (UBQLN2-Pxx) and UBQLN4 with Pxx inserted (UBQLN4+Pxx) and (B) the three full-length UBQLNs (thin lines) and corresponding constructs without the N-terminal regions (UBQLN1 32-589, UBQLN2 33-624 and UBQLN4 12-601, filled circles, thick lines) from c sat measurement as a function of temperature. Measurements were done in 20 mM NaPhosphate, 200 mM NaCl, 0.5 mM TCEP and EDTA (pH 6.8). Error bars represent SD over at least four trials from two different proteins preps.

Article Snippet: Primary antibodies include UBQLN2 rabbit mAb (Cell Signaling Technology 85509), rabbit UBQLN2 pAb (Proteintech 23449-1-AP) or UBQLN2 mouse mAb (Novus Biologicals NBP2-25164).

Techniques: Construct

Journal: bioRxiv

Article Title: Short N-terminal disordered regions and the proline-rich domain are major regulators of phase transitions for full-length UBQLN1, UBQLN2 and UBQLN4

doi: 10.1101/2023.09.27.559790

Figure Lengend Snippet: (A) Sequences and net charges of epitope tags used in this study (tyrosine residues in cyan). (B,C) Phase diagrams for (B) UBQLN2 and (C) UBQLN4 with different epitope tags from c sat measurement as a function of temperature. Myc-UBQLN2 is not included as it did not phase separate under these conditions. Measurements were done in 20 mM NaPhosphate, 200 mM NaCl, 0.5 mM TCEP and EDTA (pH 6.8). Error bars represent SD over at least four trials from two different proteins preps.

Article Snippet: Primary antibodies include UBQLN2 rabbit mAb (Cell Signaling Technology 85509), rabbit UBQLN2 pAb (Proteintech 23449-1-AP) or UBQLN2 mouse mAb (Novus Biologicals NBP2-25164).

Techniques:

Journal: bioRxiv

Article Title: Short N-terminal disordered regions and the proline-rich domain are major regulators of phase transitions for full-length UBQLN1, UBQLN2 and UBQLN4

doi: 10.1101/2023.09.27.559790

Figure Lengend Snippet: (A) Sequence alignment of the N-terminal disordered regions of UBQLN1, UBQLN2 and UBQLN4. Basic residues are in blue and acidic residues are in red. (B, C) Phase diagrams for (B) UBQLN1 and (C) UBQLN2 charge variants from c sat measurements as a function of temperature. The arrows for UBQLN2 GDE variant indicate much higher c sat than the range tested here. Measurements were done in 20 mM NaPhosphate, 200 mM NaCl, 0.5 mM TCEP and EDTA (pH 6.8). Error bars represent SD over at least four trials from two different proteins preps.

Article Snippet: Primary antibodies include UBQLN2 rabbit mAb (Cell Signaling Technology 85509), rabbit UBQLN2 pAb (Proteintech 23449-1-AP) or UBQLN2 mouse mAb (Novus Biologicals NBP2-25164).

Techniques: Sequencing, Variant Assay

Journal: European Journal of Histochemistry : EJH

Article Title: Pretreatment with geniposide mitigates myocardial ischemia/reperfusion injury by modulating inflammatory response through tLr4/NF-κb pathway

doi: 10.4081/ejh.2023.3742

Figure Lengend Snippet: Protein expression of toll-like receptor 4 (TLR4)/ nuclear factor-κB (NF-κB) (p65) signaling pathway in myocardial tissues in MI/RI-induced dysfunction rats. A ) Representative immunoblots of samples from rat ventricles subjected to different treatment groups of the myocardial tissues in rats. B Quantitative densitometric analysis of TLR4, p65, p-p65 and MyD88 protein of the myocardial tissues in rats with β-actin as an internal standard (χ±s, n=3). β-actin was used as a control, ▲▲ p<0.01 vs sham group, # p<0.05, ## p<0.01 vs MI/RI group.

Article Snippet: The primary antibodies utilized in this study were against: β-Actin (1:1000, 4967S; Cell Signaling Technology, Danvers, MA, USA), Myeloid differentiation primary response 88 (MyD88) (D80F5) Rabbit mAb (1:1000, 4283S; Cell Signaling Technology), NF-κB p65 (D14E12) XP® Rabbit mAb (1:1000, 8242S; Cell Signaling Technology), Phospho-NF-κB p65 (Ser536) (93H1) Rabbit mAb (1:1000, 3033S; Cell Signaling Technology), and TLR4 (1:300, ab217274; Abcam) followed by secondary antibodies (HRP-conjugated Goat Anti-Rabbit IgG H&L, S0001).

Techniques: Expressing, Western Blot

Journal: International Journal of Molecular Sciences

Article Title: Pharmacological Inhibition and Genetic Deletion of Cystathionine Gamma-Lyase in Mice Protects against Organ Injury in Sepsis: A Key Role of Adhesion Molecules on Endothelial Cells

doi: 10.3390/ijms241713650

Figure Lengend Snippet: Primary and secondary antibodies used in this study for Western blotting and immunofluorescence microscopy.

Article Snippet: ERK1/2 , Primary/Rabbit monoclonal , Cell Signaling, Danvers, MA, USA/137F5 , 1:2000.

Techniques: Western Blot, Immunofluorescence, Microscopy