Journal: bioRxiv

Article Title: Selective profiling of translationally active tRNAs and their dynamics under stress

doi: 10.64898/2026.03.02.709006

Figure Lengend Snippet: (A) Schematic of the experimental design. MCF-7 cells were cultured in Met-deprived media for 6 or 16 hours, alongside matched controls, with n = 3 biological replicates per condition for all experiments. Total and ribosome-associated tRNAs were analyzed using tRIBO-seq (ribo-tRNAs) and Nano-tRNA-seq (total-tRNAs). (B) Volcano plots showing differential abundance of tRNAs in the ribosome-associated (ribo-tRNAs) and total pools (total-tRNAs), for both 6-hour and 16-hour Met starvation conditions. Significance was defined as p < 0.05 with an absolute log2 fold-change ≥ 1. For simplicity, only a subset of genes are labeled; complete results are provided in Table S11 . (C) Schematic of the S-adenosylmethionine (SAM) biosynthesis and utilization cycle (see also Fig. S11A ). (D) Heatmaps depicting differential modification (methionine-starved vs. control) for Ribo-tRNAs (top) and total tRNAs (bottom) at 16 hours. Differential basecalling errors are used as a proxy to quantify differential modifications across two conditions, as previously described , . The x-axis represents nucleotide positions (5’ to 3’); the y-axis lists tRNA isoacceptors (alphabetically ordered). Common methylation sites are annotated in green. See also Fig. S12 for equivalent plots at 6h Met starvation. (E) LC–MS/MS quantification of modified nucleosides in ribo-tRNA isolated from methionine-starved and control cells. Areas were converted into picograms (pg) using standard curves for each nucleoside. Bars represent mean ± s.d. from n = 3 biological replicates per condition. P-values were calculated using a paired Student’s t -test comparing each condition to the corresponding control. Significance is indicated based on raw p -values. The left panel shows high-abundance nucleosides and the right panel low-abundance nucleosides. See also Table S13 .

Article Snippet: 100 ng of small RNA (<200 nt) fraction, separated as described above, were digested with 1 μl of the Nucleoside Digestion Mix (New England BioLabs, #M0649S) and the mixture was incubated at 37 °C for 1 h. Samples were analyzed using an Orbitrap Eclipse Tribrid mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) coupled to an EASY-nLC 1200 (Thermo Fisher Scientific (Proxeon), Odense, Denmark).

Techniques: Cell Culture, Labeling, Modification, Control, Methylation, Liquid Chromatography with Mass Spectroscopy, Isolation

Journal: International Journal of Molecular Sciences

Article Title: Lymphoid Organ Proteomes Identify Therapeutic Efficacy Biomarkers Following the Intracavitary Administration of Curcumin in a Highly Invasive Rat Model of Peritoneal Mesothelioma

doi: 10.3390/ijms22168566

Figure Lengend Snippet: Purine nucleoside phosphorylase (PNPH) in lymph nodes. ( A ) Proteomic analysis. ( B , C ) Immunohistochemical staining with anti-PNPH antibody of lymph nodes from two representative rats of G2 (top) and G3 (bottom) groups (general views in inserts). Photographs in ( B ) illustrate the differences in staining intensity of PNPH+ cells present in the medullary sinus. Photographs in ( C ) show the presence of numerous PNPH+ cells in the outer cortex and some in the inner cortex in G3 rat (absent in G2 rat). Yellow arrows indicate probable macrophages/dendritic cells in the germinal center. Scale bars represent 50 µm.

Article Snippet: Complementary immunohistochemical analyses were conducted with rabbit anti-PDCD4 (NBP1-76738) and anti-PNPH (NBP1-82541) antibodies (Novus Biologicals, Centennial, CO, USA).

Techniques: Immunohistochemical staining, Staining

Journal: Oncology Research

Article Title: PNP as a Metabolic and Prognostic Driver of Breast Cancer Aggressiveness: Insights from Patient Tissue and Cell Models

doi: 10.32604/or.2025.070808

Figure Lengend Snippet: Spearman’s rank correlation between PNP and EMT, hormonal, and proliferation markers. ( A – H ) EMT markers, including ( A ) Claudin, ( B ) E-cadherin, ( C ) N-cadherin, ( D ) Vimentin, ( E ) Fibronectin, ( F ) MMP-9, ( G ) Snail, and ( H ) Slug. ( I–K ) Hormonal markers including ( I ) estrogen receptor, ( J ) progesterone receptor, and ( K ) HER-2. ( L ) Proliferation marker Ki-67. The figure was obtained using the TIMER 2 web tool. rho denotes Spearman’s rank correlation coefficient

Article Snippet: The membrane was then incubated with primary antibodies against PNP (dilution 1:1000) (#MAB6486, R&D Systems, Minneapolis, MN, USA), HER-2 (dilution 1:1000) (# AB214275 , Abcam, Cambridge, UK), and β-actin (dilution 1:2000) (#4970, Cell Signaling Technology, Danvers, MA, USA) at 4°C overnight.

Techniques: Marker

Journal: Oncology Research

Article Title: PNP as a Metabolic and Prognostic Driver of Breast Cancer Aggressiveness: Insights from Patient Tissue and Cell Models

doi: 10.32604/or.2025.070808

Figure Lengend Snippet: Scatter plots showing correlations between PNP expression and EMT markers, hormone receptors, and proliferation markers in BRCA (TCGA-BRCA dataset) as analyzed using GEPIA2. ( A–H ) EMT markers, including ( A ) Claudin, ( B ) E-cadherin, ( C ) N-cadherin, ( D ) Vimentin, ( E ) Fibronectin, ( F ) MMP-9, ( G ) Snail, and ( H ) Slug. ( I–K ) Hormonal markers including ( I ) estrogen receptor, ( J ) progesterone receptor, and ( K ) HER-2. ( L ) Proliferation marker Ki-67

Article Snippet: The membrane was then incubated with primary antibodies against PNP (dilution 1:1000) (#MAB6486, R&D Systems, Minneapolis, MN, USA), HER-2 (dilution 1:1000) (# AB214275 , Abcam, Cambridge, UK), and β-actin (dilution 1:2000) (#4970, Cell Signaling Technology, Danvers, MA, USA) at 4°C overnight.

Techniques: Expressing, Marker

Journal: Oncology Research

Article Title: PNP as a Metabolic and Prognostic Driver of Breast Cancer Aggressiveness: Insights from Patient Tissue and Cell Models

doi: 10.32604/or.2025.070808

Figure Lengend Snippet: Analysis of transcriptomics data of 2509 invasive BC patients in relation to PNP expression and BC subtypes, stages, and grades. The association between PNP mRNA expression and ( A ) BC subtypes Luminal: luminal A (ER+/PR+, HER2−) and luminal B (ER+/PR+, HER2−), and HER−2 positive: luminal B (ER+/PR+, HER2+) and HER2 overexpression (ER−/PR−, HER2+) and TNBC (ER−/PR−, HER2−), ( B ) ER status, ( C ) PR status, ( D ) HER-2 status, ( E ) Histologic grades, and ( F ) BC stages. Bar charts of patients’ percentages according to high PNP expression and low PNP expression groups

Article Snippet: The membrane was then incubated with primary antibodies against PNP (dilution 1:1000) (#MAB6486, R&D Systems, Minneapolis, MN, USA), HER-2 (dilution 1:1000) (# AB214275 , Abcam, Cambridge, UK), and β-actin (dilution 1:2000) (#4970, Cell Signaling Technology, Danvers, MA, USA) at 4°C overnight.

Techniques: Expressing, Over Expression

Journal: Oncology Research

Article Title: PNP as a Metabolic and Prognostic Driver of Breast Cancer Aggressiveness: Insights from Patient Tissue and Cell Models

doi: 10.32604/or.2025.070808

Figure Lengend Snippet: Analysis of invasive breast cancer patients’ tissues based on protein expression of PNP in relation to BC subtypes, stages, and grades. The association between PNP protein expression and ( A ) breast cancer subtypes Luminal: luminal A (ER+/PR+, HER-2−) and luminal B (ER+/PR+, HER-2−), and HER−2 positive: luminal B (ER+/PR+, HER−2+) and HER−2 overexpression (ER−/PR−, HER−2+) and triple negative (ER−/PR−, HER-2−), ( B ) ER status, ( C ) PR status, ( D ) HER−2 status, ( E ) Histologic grades, and ( F ) BC stages. Bar charts of patients’ percentages according to high PNP expression and low PNP expression groups

Article Snippet: The membrane was then incubated with primary antibodies against PNP (dilution 1:1000) (#MAB6486, R&D Systems, Minneapolis, MN, USA), HER-2 (dilution 1:1000) (# AB214275 , Abcam, Cambridge, UK), and β-actin (dilution 1:2000) (#4970, Cell Signaling Technology, Danvers, MA, USA) at 4°C overnight.

Techniques: Expressing, Over Expression

Journal: Oncology Research

Article Title: PNP as a Metabolic and Prognostic Driver of Breast Cancer Aggressiveness: Insights from Patient Tissue and Cell Models

doi: 10.32604/or.2025.070808

Figure Lengend Snippet: Correlation between PNP and HER-2 in SKBR3 cells. ( A ) Western blot analysis showing protein expression levels of HER-2 and PNP in SKBR3 cells treated with vehicle control (CTL), BCX-1777 (a PNP inhibitor), or trastuzumab (a HER-2 inhibitor). Quantification of protein expression levels of ( B ) PNP and ( C ) HER-2 in SKBR3 cells treated as in ( A ). ( D ) Western blot showing HER-2 and PNP protein levels after siRNA-mediated knockdown of PNP (siPNP) or negative control (siNC). Quantification of ( E ) PNP and ( F ) HER-2 expression in siPNP versus siNC conditions. ( G ) SKBR3 cell viability was assessed using the MTT assay and expressed as a percentage relative to untreated control (CTL) cells. Data shown are representative blots from three independent biological replicates ( n = 3). Quantification represents mean ± SD. The data were analyzed using Student’s t -test or one-way ANOVA. p- value < 0.05 was considered significant. * reveals that p -value < 0.05, ** reveals that p -value < 0.01, *** reveals that p -value < 0.001, **** reveals that p -value < 0.0001. Original blots are presented in

Article Snippet: The membrane was then incubated with primary antibodies against PNP (dilution 1:1000) (#MAB6486, R&D Systems, Minneapolis, MN, USA), HER-2 (dilution 1:1000) (# AB214275 , Abcam, Cambridge, UK), and β-actin (dilution 1:2000) (#4970, Cell Signaling Technology, Danvers, MA, USA) at 4°C overnight.

Techniques: Western Blot, Expressing, Control, Knockdown, Negative Control, MTT Assay

Journal: Computers in Biology and Medicine

Article Title: Identification of FDA approved drugs and nucleoside analogues as potential SARS-CoV-2 A1pp domain inhibitor: An in silico study

doi: 10.1016/j.compbiomed.2020.104185

Figure Lengend Snippet: Surface structure of lead FDA approved drug, nucleoside inhibitor and natural substrate at SARS-CoV-2 A1pp domain active site. (A) Surface structure of lactobionic acid at ADP-ribose-1″-phosphatase active site. (B) Surface structure of NA 1 at ADP-ribose-1″-phosphatase active site. (C) Surface structure of adenosine-5-diphosphoribose at ADP-ribose-1″-phosphatase active site. (D) 2D structure of lactobionic acid. (E) 2D structure of NA 1 . (F) 2D structure of adenosine-5-diphosphoribose.

Article Snippet: The structures of FDA approved drugs and nucleoside analogues were downloaded from selleckchem ( https://www.selleckchem.com/ ) in. sdf format and converted to different formats using Open Babel software.

Techniques: