Journal: International Journal of Oncology

Article Title: Disruption of serine/threonine protein phosphatase 5 inhibits tumorigenesis of urinary bladder cancer cells

doi: 10.3892/ijo.2017.3997

Figure Lengend Snippet: High expression of PPP5C is associated with T stage, malignant degree and prognosis in BCa as analyzed by ONCOMINE microarray database. (A) Meta-analysis of the PPP5C expression between the BCa and the normal urothelial tissue from 3 microarray datasets containing 7 groups (P<0.001). (B) Each expression difference of the bladder cancer and normal tissue in the Sanchez-Carbayo Bladder 2 dataset (P<0.0001), Lee Bladder dataset (P=0.028), Dyrskjot Bladder 3 (P<0.0001). (C) The Kaplan-Meier analysis on the correlation between the PPP5C and the survival using the Als dataset (P=0.0007). (D and E) The two microarray datasets (Blaveri bladder 2 and Dyrskjot Bladder) show that the expression of PPP5C in T stage ≥T1 was higher than that in Ta. (F) The Blaveri bladder 2 dataset indicated that the expression of PPP5C in BCa of high-grade malignancy was higher than that in BCa of low-grade malignancy (P=0.0385).

Article Snippet: Then, the membranes were incubated with the following primary antibodies: PPP5C (#:11715-1-AP; Proteintech Group, Chicago, IL, USA), CDK4 (#:11026-1-AP; Proteintech Group), c-Myc (#:sc-40; Santa Cruz Biotechnology, Santa Cruz, CA, USA), p27 (#:3686; Cell Signaling Technology, Danvers, MA, USA), BAD (#:10435-1-AP; Proteintech Group), Beclin1 (#:3495; Cell Signaling Technology) and GAPDH (#:10494-1-AP; Proteintech Group) for 12 h at 4°C.

Techniques: Expressing, Microarray

Journal: International Journal of Oncology

Article Title: Disruption of serine/threonine protein phosphatase 5 inhibits tumorigenesis of urinary bladder cancer cells

doi: 10.3892/ijo.2017.3997

Figure Lengend Snippet: PPP5C expression and patient characteristics of ALS Bladder dataset.

Article Snippet: Then, the membranes were incubated with the following primary antibodies: PPP5C (#:11715-1-AP; Proteintech Group, Chicago, IL, USA), CDK4 (#:11026-1-AP; Proteintech Group), c-Myc (#:sc-40; Santa Cruz Biotechnology, Santa Cruz, CA, USA), p27 (#:3686; Cell Signaling Technology, Danvers, MA, USA), BAD (#:10435-1-AP; Proteintech Group), Beclin1 (#:3495; Cell Signaling Technology) and GAPDH (#:10494-1-AP; Proteintech Group) for 12 h at 4°C.

Techniques: Expressing

Journal: International Journal of Oncology

Article Title: Disruption of serine/threonine protein phosphatase 5 inhibits tumorigenesis of urinary bladder cancer cells

doi: 10.3892/ijo.2017.3997

Figure Lengend Snippet: Lentivirus-mediated interference downregulates the expression of PPP5C in urinary bladder cancer cells. (A) T24 and BT5637 cells were examined by fluorescence microscopy after lentivirus infection for 72 h. (B and C) Knock-down efficiency of PPP5C mRNA level in T24 and BT5637 infected by Lv-shPPP5C was determined by real-time qPCR ( *** P<0.001). (D and E) The protein level of PPP5C was downregulated in T24 and BT5637 cells. Lv-shCon, lentivirus-mediated non-silencing shRNA; Lv-shPPP5C, lentivirus-mediated non-silencing shPPP5C. Data were presented as mean ± SD from at least three experiments.

Article Snippet: Then, the membranes were incubated with the following primary antibodies: PPP5C (#:11715-1-AP; Proteintech Group, Chicago, IL, USA), CDK4 (#:11026-1-AP; Proteintech Group), c-Myc (#:sc-40; Santa Cruz Biotechnology, Santa Cruz, CA, USA), p27 (#:3686; Cell Signaling Technology, Danvers, MA, USA), BAD (#:10435-1-AP; Proteintech Group), Beclin1 (#:3495; Cell Signaling Technology) and GAPDH (#:10494-1-AP; Proteintech Group) for 12 h at 4°C.

Techniques: Expressing, Fluorescence, Microscopy, Infection, Knockdown, shRNA

Journal: International Journal of Oncology

Article Title: Disruption of serine/threonine protein phosphatase 5 inhibits tumorigenesis of urinary bladder cancer cells

doi: 10.3892/ijo.2017.3997

Figure Lengend Snippet: Lentivirus-mediated knockdown of PPP5C suppresses cell viability of urinary bladder cancer cells. (A and B) After infection with Lv-shCon or Lv-shPPP5C, the growth curves of T24 and BT5637 cells were determined by MTT assay. Data are presented as mean ± SD from at least three experiments ( *** P<0.001). (C and D) Representative images of T24 and BT5637 cells colony formation under micro- and macro-views after infection with Lv-shCon or Lv-shPPP5C. (E and F) The number of colonies formed in T24 and BT5637 cells treated as in (C and D). Data are presented as mean ± SD from at least three experiments ( * P<0.05, *** P<0.001).

Article Snippet: Then, the membranes were incubated with the following primary antibodies: PPP5C (#:11715-1-AP; Proteintech Group, Chicago, IL, USA), CDK4 (#:11026-1-AP; Proteintech Group), c-Myc (#:sc-40; Santa Cruz Biotechnology, Santa Cruz, CA, USA), p27 (#:3686; Cell Signaling Technology, Danvers, MA, USA), BAD (#:10435-1-AP; Proteintech Group), Beclin1 (#:3495; Cell Signaling Technology) and GAPDH (#:10494-1-AP; Proteintech Group) for 12 h at 4°C.

Techniques: Knockdown, Infection, MTT Assay

Journal: International Journal of Oncology

Article Title: Disruption of serine/threonine protein phosphatase 5 inhibits tumorigenesis of urinary bladder cancer cells

doi: 10.3892/ijo.2017.3997

Figure Lengend Snippet: Knock-down of the PPP5C level inhbits the growth of BCa in vivo . (A and C) The subcutaneous xenograft nude mice and the tumor sample were collected and imaged. (B and D) The tumor size and weight were significantly decreased in nude mice infected with lv-shPPP5C-T24 cell (n=6) as compared with those in nude mice infected with lv-shCon-T24 (n=6) ( * P<0.05, ** P<0.01, *** P<0.001).

Article Snippet: Then, the membranes were incubated with the following primary antibodies: PPP5C (#:11715-1-AP; Proteintech Group, Chicago, IL, USA), CDK4 (#:11026-1-AP; Proteintech Group), c-Myc (#:sc-40; Santa Cruz Biotechnology, Santa Cruz, CA, USA), p27 (#:3686; Cell Signaling Technology, Danvers, MA, USA), BAD (#:10435-1-AP; Proteintech Group), Beclin1 (#:3495; Cell Signaling Technology) and GAPDH (#:10494-1-AP; Proteintech Group) for 12 h at 4°C.

Techniques: Knockdown, In Vivo, Infection

Journal: International Journal of Oncology

Article Title: Disruption of serine/threonine protein phosphatase 5 inhibits tumorigenesis of urinary bladder cancer cells

doi: 10.3892/ijo.2017.3997

Figure Lengend Snippet: Disruption of PPP5C expression causes cell cycle arrest in bladder cancer cells. (A) Flow cytometric analysis showing cell cycle distribution of T24 and BT5637 cells infected by Lv-shCon or Lv-shPPP5C. (B) Cell percentages in G0/G1, S and G2/M of T24 and BT5637 cells treated as in (A) were analyzed statistically ( * P<0.05, ** P<0.01, *** P<0.001).

Article Snippet: Then, the membranes were incubated with the following primary antibodies: PPP5C (#:11715-1-AP; Proteintech Group, Chicago, IL, USA), CDK4 (#:11026-1-AP; Proteintech Group), c-Myc (#:sc-40; Santa Cruz Biotechnology, Santa Cruz, CA, USA), p27 (#:3686; Cell Signaling Technology, Danvers, MA, USA), BAD (#:10435-1-AP; Proteintech Group), Beclin1 (#:3495; Cell Signaling Technology) and GAPDH (#:10494-1-AP; Proteintech Group) for 12 h at 4°C.

Techniques: Disruption, Expressing, Infection

Journal: International Journal of Oncology

Article Title: Disruption of serine/threonine protein phosphatase 5 inhibits tumorigenesis of urinary bladder cancer cells

doi: 10.3892/ijo.2017.3997

Figure Lengend Snippet: Apoptotic cells are increased after PPP5C silencing. (A) Apoptosis of T24 and BT5637 was analyzed in lv-shCon and lv-shPPP5C groups using flow cytometry and Annexin V/PI staining. (B) Early apoptosis (V + /PI − ) and late apoptosis (V + /PI + ) of the T24 and BT5637 cells were statistically analyzed ( * P<0.05, **P<0.01, *** P<0.001).

Article Snippet: Then, the membranes were incubated with the following primary antibodies: PPP5C (#:11715-1-AP; Proteintech Group, Chicago, IL, USA), CDK4 (#:11026-1-AP; Proteintech Group), c-Myc (#:sc-40; Santa Cruz Biotechnology, Santa Cruz, CA, USA), p27 (#:3686; Cell Signaling Technology, Danvers, MA, USA), BAD (#:10435-1-AP; Proteintech Group), Beclin1 (#:3495; Cell Signaling Technology) and GAPDH (#:10494-1-AP; Proteintech Group) for 12 h at 4°C.

Techniques: Flow Cytometry, Staining

Journal: bioRxiv

Article Title: Evaluating the reliability of tools for mRNA annotation and IRES studies

doi: 10.64898/2026.03.29.707813

Figure Lengend Snippet: (A) A-cap / stemloop IRES reporter RNA carrying the negative control “scramble 1” sequence was mixed into a polysome lysate made from HEK293T cells for five minutes on ice and loaded on a sucrose gradient. (B) The sucrose gradient was fractionated and cDNA was prepared from groups of fractions as shown (numbered 1 -6). qRT-PCR was performed to quantify the exogenous “scramble 1” RNA across the fractions, as compared to endogenous Gapdh mRNA. The “scramble 1” transcript migrated into polysomal fractions 4-6, even though it is not translated .

Article Snippet: The ARCA m 7 G-cap analog (New England Biolabs; S1411) was used at a 4:1 ratio to GFP for transcription of T7-nluc constructs, while an A-cap analog (New England Biolabs S1406), was used to generate T7HP-nluc IRES reporter RNAs.

Techniques: Negative Control, Sequencing, Quantitative RT-PCR

Journal: Nucleic Acids Research

Article Title: Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic sinefungin

doi: 10.1093/nar/gkaf538

Figure Lengend Snippet: Structures of K. lactis RNA cap methyltransferase in complexes with products SAH and m 7 GTP. ( A ) Schmatic outline of the experimental setup for methylation assays. Methylation of substrate (m 7 GpppA) was detected by separating reactions products (in red and blue) using a high-performance liquid chromatography (HPLC) column coupled to a triple quadrupole (QQQ) MS, which detects product ions (see the “Materials and methods” section). Quantification was achieved by normalizing ion counts to an internal standard, l -tryptophan. The ratio of m 7 GpppA ion counts to l -tryptophan ion counts yielded the internal standard ratio (ISTD). A range of m 7 GpppA calibration standards (with constant l -tryptophan) provided a linear calibration curve between ISTD and m 7 GpppA concentration. Sample ISTDs were then used to interpolate a discrete m 7 GpppA concentration from the calibration curve. ( B ) Methylation activities of wild-type (purple circles) and two truncated Kl Abd1 variants ( Kl Abd1Δ116, pink circles; and Kl Abd1Δ137, dark pink circles) with GpppA substrate (see the “Materials and methods” section). Error bars (one standard deviation) are calculated from three independent experiments performed in triplicate. ( C ) A view of the Kl Abd1 structure (colored purple) as a ribbon with arrows for β-strands and wide ribbons for helices. A transparent molecular surface envelops the structure. N and C denote amino and carboxyl termini, respectively. Bound SAH in the methyl donor site is shown in stick representation (green). ( D ) A closeup view of the methyl donor site of Kl Abd1–SAH complex. ( E ) A view of the methyl acceptor site of Kl Abd1 bound to m 7 GTP (stick representation in cyan). Bound adenine in the methyl donor site is shown in stick representation (green) and rest of the unresolved substrate/product is depicted in thin gray line. Side chains shown in stick representation, and waters are denoted by red spheres. Atomic contacts are indicated by dashed lines with distances. ( F ) Aligned primary structures of cap methyltransferases from K. lactis ( Kl Abd1), S. cerevisiae ( Sc Abd1), E. cuniculi (Ecm1), and Homo sapiens (RNMT). The secondary structure elements of Kl Abd1 are shown above the amino acid sequences, with α-helices depicted as cylinders and β-strand as arrows. Gaps in the alignments are indicated by “•”. Side-chain identity/similarity is denoted by shading and letter color (purple shade conserved in all; purple letters conserved in most). A predicted disordered region N-terminal to the catalytic domain is denoted by a purple dashed line above the alignment. Kl Abd1 amino acids that contact SAH and m 7 GTP are indicated by green and orange circles, respectively. A conserved tyrosine in β11 that interacts with the cap guanosine is outlined in cyan.

Article Snippet: Solutions of SAM (Cayman Chemical), SAH (Millipore-Sigma), SFG (Santa Cruz Biotechnology), GTP (Jena Bioscience), m 7 GTP (Millipore-Sigma), GpppA (Jena Bioscience), and m 7 GpppA (Jena Bioscience) were prepared in 300 mM HEPES buffer (pH 7.5), and concentrations were determined from the absorbance at 260 nm using the following extinction coefficients (M −1 cm −1 ): SAM, 16000; SAH, 15400; SFG, 16000; GTP, 13700; m 7 GTP, 9800; GpppA, 27000; and m 7 GpppA, 22700.

Techniques: Methylation, High Performance Liquid Chromatography, Targeted Proteomics, Concentration Assay, Standard Deviation

Journal: Nucleic Acids Research

Article Title: Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic sinefungin

doi: 10.1093/nar/gkaf538

Figure Lengend Snippet: Activity and inhibition of S. cerevisiae Abd1. ( A ) Methylation activities of full-length wild-type (WT) Sc Abd1 (light gray triangles), two truncated Sc Abd1 variants ( Sc Abd1Δ119, gray circles; and Sc Abd1Δ140, dark gray squares) and SFG-resistant Sc Abd1-E124K-K163R-K311R-F387Y-Y416F variant (red squares) with GpppA substrate (see the “Materials and methods” section). Error bars (one standard deviation) are calculated from three independent experiments performed in triplicate. ( B ) Inhibition of methylation activities (three independent experiments) of Sc Abd1WT (light gray circles), SFG-resistant variants of Sc Abd1 ( Sc Abd1-L59P-Y416C, green circles; Sc Abd1-E124K-K163-K311R-F387Y-Y416, red circles; Sc Abd1-Y416N-R422H, black circles; Sc Abd1-Y416A, orange circles) with SAH. Reaction mixtures containing 250 nM enzyme preparations were incubated with 100 μM SAM, 250 μM GpppA, and variable concentrations (0, 3.125, 12.5, 25, 50, 100, 200, and 800 μM; see the “Materials and methods” section) of SAH at 30°C in buffer consisting of 50 mM Tris (pH 8.2), 200 mM NaCl, and 5 mM βME. After 20 min, 10 μl reaction samples were quenched with 10 μl of quenching solution containing 100 mM H 2 SO 4 and 50 μM l -tryptophan. Concurrently, m 7 GpppA standards were quenched in quenching solution. ( C ) Inhibition of methylation activities of wild-type and SFG-resistant variants of Sc Abd1 with SFG as shown in panel (B). Reaction mixture containing 250 nM enzyme preparations was incubated with 100 μM SAM, 250 μM GpppA, and variable concentrations (0, 15.6, 31.25, 62.5, 125, 250, and 500 nM for the wild-type proteins; 0, 100 nM, 500 nM, 750 nM, 1.2 μM, 1.7 μM, 2.2 μM, and 4.0 μM for the variants; see the “Materials and methods” section) of SFG at 30°C in buffer consisting of 50 mM Tris (pH 8.2), 200 mM NaCl, and 5 mM βME. After 20 min, 10 μl reaction samples were quenched with 10 μl of quenching solution containing 100 mM H 2 SO 4 and 50 μM l -tryptophan. ( D ) Ratios of IC 50 values of wild-type and variant Sc Abd1 and Kl Abd1 between SAH and SFG with GpppA substrate. Significance between the wild-type and resistant variants determined by ordinary one-way ANOVA (**** signifies adjusted P -value <.0001). ( E ) IC 50 values for SAH (μM) and SFG (nM) obtained from panels (B) and (C) for Sc Abd1WT (gray), Sc Abd1-L59P-Y416C (green), Sc Abd1-E124K-K163-K311R-F387Y-Y416 (red), Sc Abd1-Y416N-R422H (black), and Sc Abd1-Y416A (orange).

Article Snippet: Solutions of SAM (Cayman Chemical), SAH (Millipore-Sigma), SFG (Santa Cruz Biotechnology), GTP (Jena Bioscience), m 7 GTP (Millipore-Sigma), GpppA (Jena Bioscience), and m 7 GpppA (Jena Bioscience) were prepared in 300 mM HEPES buffer (pH 7.5), and concentrations were determined from the absorbance at 260 nm using the following extinction coefficients (M −1 cm −1 ): SAM, 16000; SAH, 15400; SFG, 16000; GTP, 13700; m 7 GTP, 9800; GpppA, 27000; and m 7 GpppA, 22700.

Techniques: Activity Assay, Inhibition, Methylation, Variant Assay, Standard Deviation, Incubation

Journal: Nucleic Acids Research

Article Title: Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic sinefungin

doi: 10.1093/nar/gkaf538

Figure Lengend Snippet: Structure of K. lactis Abd1 bound to inhibitor SFG and SFG plus GTP. ( A ) SAH inhibition. The extent of methylation of GpppA by wild-type Kl Abd1 was quantified (see the “Materials and methods” section) in the presence of increasing concentrations (0, 3.125, 12.5, 25, 50, 100, 200, and 800 μM) of SAH and the obtained relative activities (%) for the enzyme (green circles) were plotted as a function SAH concentrations to determine the IC 50 value (indicated). ( B ) SFG inhibition. The extent of methylation of GpppA by wild-type Kl Abd1 was quantified (see the “Materials and methods” section) in the presence of increasing concentrations (0, 15.6, 32.25, 62.5, 125, 250, and 500 nM) of SFG and the relative activities (%) for Kl Abd1 (light yellow circles) were plotted as a function SFG concentrations to determine the IC 50 value (indicated). Error bars (one standard deviation) are calculated from three independent experiments performed in triplicate. ( C ) A view of the methyl donor site of Kl Abd1 bound to SFG shown in stick representation and colored light yellow. ( D ) A closeup view of the methyl acceptor site of Kl Abd1 bound to SFG (as in panel B) and GTP (stick representation in cyan). Side chains are shown in stick representation (as in Fig. ), and waters are denoted by red spheres. Atomic contacts are indicated by dashed lines with distances.

Article Snippet: Solutions of SAM (Cayman Chemical), SAH (Millipore-Sigma), SFG (Santa Cruz Biotechnology), GTP (Jena Bioscience), m 7 GTP (Millipore-Sigma), GpppA (Jena Bioscience), and m 7 GpppA (Jena Bioscience) were prepared in 300 mM HEPES buffer (pH 7.5), and concentrations were determined from the absorbance at 260 nm using the following extinction coefficients (M −1 cm −1 ): SAM, 16000; SAH, 15400; SFG, 16000; GTP, 13700; m 7 GTP, 9800; GpppA, 27000; and m 7 GpppA, 22700.

Techniques: Inhibition, Methylation, Standard Deviation