Journal: International journal of molecular sciences

Article Title: Refining Evaluation of Bone Mass and Adipose Distribution in Dunnigan Syndrome.

doi: 10.3390/ijms241713118

Figure Lengend Snippet: Figure 3. Osteoclast differentiation derived from peripheral blood mononuclear cells from controls and DS patients. (A) An area of osteoclasts developed in a culture in the presence of MCSF + RANKL and MCSF + RANKL + chemerin. (B) The number of osteoclast cells according to the type of medium added in sequence. Each step of the sequence was cultured in 3 distinct wells for each subject analyzed. The final result is the average sum of controls and patients. (C) The appearance of the osteoclast cells developed in a culture supplemented with MCSF + RANKL and (D) MCSF + RANKL + chemerin in a DS subject. Osteoclasts must have 3 or more nuclei. * p < 0.05. Abbreviations: MCSF, macrophage colony-stimulating factor; RANKL, receptor activator of nuclear factor kappa-B ligand; DS, Dunnigan syndrome.

Article Snippet: These monocytes were cultured in 3 × 3 wells in 96-well plates with α-MEM containing 10% FBS added sequentially in triplets with 25 ng/mL of human macrophage colony-stimulating factor (MCSF) (R&D systems, catalog 216-MCC, Minneapolis, MN, USA), 25 ng/mL of receptor activator of nuclear factor kappa-B ligand (RANKL) (R&D systems, catalog 390-TN, Minneapolis, MN, USA) and 50 ng/mL of chemerin (R&D systems, catalog 2324-CM, Minneapolis, MN, USA) to stimulate osteoclasts.

Techniques: Derivative Assay, Sequencing, Cell Culture

Journal: BMC Complementary Medicine and Therapies

Article Title: Inhibitory effects of the flavonoids extracted from Pollen Typhae on palmitic acid-induced NLRP3 inflammasome activation in macrophages involving AMPK-mediated lipid metabolism

doi: 10.1186/s12906-025-05024-4

Figure Lengend Snippet: Pollen Typhae flavonoids attenuate PA-induced NLRP3 inflammasome activation in macrophages. ( A ) After pretreatment with or without LPS (1 ng/ml) for 3 h, RAW264.7 macrophages were stimulated with PA (0.125 ~ 0.5 mM) for 16 h, IL-1β and IL-18 in culture supernatants were analyzed by ELISA. ( B ) The macrophages were pretreated with LPS (1 ng/ml) for 3 h, followed by PA (0.5 mM) treatment for 16 h, the protein expression of NLRP3, Caspase-1, and Caspase-1 p10 was analyzed by western blotting. The uncropped blots were presented in Supplementary Fig. . ( C ) RAW264.7 macrophages were treated with PTF (0 ~ 0.5 mg/ml), TYP (0 ~ 100 µM) or I3ON (0 ~ 100 µM) for 16 and 20 h, the cell viability was detected by CCK-8 assay. * P < 0.05, ** P < 0.01 versus 0.0 mg/ml PTF (0.0 µM TYP or I3ON). ( D ) The macrophages were pretreated with LPS (1 ng/ml) or plus different concentrations of PTF (0.03125 ~ 0.5 mg/ml), TYP (10 ~ 100 µM), I3ON (10 ~ 100 µM) for 3 h before exposure to PA (0.5 mM) for 16 h, IL-1β and IL-18 in culture supernatants were checked by ELISA. ( E and F ) The macrophages were pretreated with LPS (1 ng/ml) or plus PTF (0.5 mg/ml), TYP (100 µM), AICAR (2 mM), MCC950 (10 µM) for 3 h followed by exposure to PA (0.5 mM) for 16 h, the protein (E) and gene expression (F) of NLRP3, Caspase-1 and IL-1β were checked by western blotting and Real-time PCR, respectively. The uncropped/unedited blots were presented in Supplementary Fig. . Each column shows the mean with SD ( n = 3–7). * P < 0.05, ** P < 0.01 versus LPS (1 ng/ml); # P < 0.05, ## P < 0.01 versus LPS (1 ng/ml) plus PA (0.5 mM)

Article Snippet: The macrophages were pre-exposed to LPS (1 ng/ml) or/and PTF (0.5 mg/ml), TYP (100 μM), AICAR (2 mM, Beyotime, Shanghai, China), MCC950 (10 μM, Cell Signaling Technology, Danvers, MA, USA), PF-05175157 (10 μM, GlpBio Technology, Montclair, CA, USA) for 3 h before treatment with PA (0.5 mM) for 16 h. The cells were harvested to obtain total protein.

Techniques: Activation Assay, Enzyme-linked Immunosorbent Assay, Expressing, Western Blot, CCK-8 Assay, Gene Expression, Real-time Polymerase Chain Reaction

Journal: BMC Complementary Medicine and Therapies

Article Title: Inhibitory effects of the flavonoids extracted from Pollen Typhae on palmitic acid-induced NLRP3 inflammasome activation in macrophages involving AMPK-mediated lipid metabolism

doi: 10.1186/s12906-025-05024-4

Figure Lengend Snippet: Effects of PTF, AMPK agonist, ACC inhibitor and antioxidant on PA-induced Caspase-1 activity in macrophages. RAW264.7 macrophages were pretreated with LPS (1 ng/ml) or plus PTF (0.5 mg/ml), TYP (100 µM), PF-05175157 (10 µM), AICAR (2 mM), Compound C (10 µM), NAC (10 mM), MCC950 (10 µM) for 3 h before treatment with PA (0.5 mM) for 16 h, the Caspase-1 activity in culture supernatants ( A ) and the macrophages ( B ) was analyzed by bioluminescent method. Each column shows the mean with SD ( n = 3). * P < 0.05, ** P < 0.01 versus LPS (1 ng/ml); # P < 0.05, ## P < 0.01 versus LPS (1 ng/ml) plus PA (0.5 mM); § P < 0.05 versus LPS (1 ng/ml) plus PA (0.5 mM) and PTF (0.5 mg/ml)

Article Snippet: The macrophages were pre-exposed to LPS (1 ng/ml) or/and PTF (0.5 mg/ml), TYP (100 μM), AICAR (2 mM, Beyotime, Shanghai, China), MCC950 (10 μM, Cell Signaling Technology, Danvers, MA, USA), PF-05175157 (10 μM, GlpBio Technology, Montclair, CA, USA) for 3 h before treatment with PA (0.5 mM) for 16 h. The cells were harvested to obtain total protein.

Techniques: Activity Assay

Journal: Genes & Diseases

Article Title: Integrative high-throughput studies to develop novel targets and drugs for the treatment of advanced prostate cancer

doi: 10.1016/j.gendis.2025.101732

Figure Lengend Snippet: Enhanced CDRs correlated with prostate cancer prognosis. (A) Visualization of core genes' dependency in different prostate cancer cells with CRISPR-Cas9 and siRNA screening. (B, C) Survival analysis of CDRs in different CRPC patient cohorts. (D) The relative expression of CDRs in normal prostate tissues and prostate cancer tissues in the TCGA-PRAD cohort. Gleason score and tumor stage correlation analysis of CDRs in different prostate cancer patient cohorts. All prostate patient cohorts were indicated in the corresponding panels. CDRs refers to CDC20 (cell division cycle 20), DTL (denticleless E3 ubiquitin protein ligase), and RRM2 (ribonucleotide reductase M2).

Article Snippet: Three guide RNAs (gRNA) for each target, including RB1, E2F1, CDC20, RRM2, and DTL, were designed, generated, and cloned into CRSIPR-Cas13 corresponding gRNA backbone (Addgene, 109053).

Techniques: CRISPR, Expressing, Ubiquitin Proteomics

Journal: Genes & Diseases

Article Title: Integrative high-throughput studies to develop novel targets and drugs for the treatment of advanced prostate cancer

doi: 10.1016/j.gendis.2025.101732

Figure Lengend Snippet: CDRs linked with neuroendocrine features in prostate cancer cohorts. (A) The Venn diagram illustrates the genes specifically enhanced in prostate cancer compared with normal prostate tissues and NEPC compared with adenocarcinoma. (B, C) The relative expression of CDRs in NEPC compared with adenocarcinoma in different prostate cancer cohorts. (D) Correlation analysis of CDRs with NE score. The red indicates the higher NE score. (E, F) Pearson correlation analysis of CDRs with NE score CRPC cohort. (G) The heatmap indicates the relative expression of CDRs and AR, as well as KLK3, a transcription activity indication of AR. CDRs refers to CDC20 (cell division cycle 20), DTL (denticleless E3 ubiquitin protein ligase), and RRM2 (ribonucleotide reductase M2). NEPC, neuroendocrine prostate cancer; NE, neuroendocrine; AR, androgen receptor; KLK3, kallikrein-related peptidase 3.

Article Snippet: Three guide RNAs (gRNA) for each target, including RB1, E2F1, CDC20, RRM2, and DTL, were designed, generated, and cloned into CRSIPR-Cas13 corresponding gRNA backbone (Addgene, 109053).

Techniques: Expressing, Activity Assay, Ubiquitin Proteomics

Journal: Genes & Diseases

Article Title: Integrative high-throughput studies to develop novel targets and drugs for the treatment of advanced prostate cancer

doi: 10.1016/j.gendis.2025.101732

Figure Lengend Snippet: CDRs ablation suppressed prostate cancer cell proliferation. (A) The circuit diagram illustrates the correlation among CDRs co-expressed gene sets. (B) Venn analysis of the overlap of CDRs co-expressed genes. (C) The heatmap shows the relative expression of CDRs overlapped co-expressed genes in patients with NE signature high and low groups. (D – F) The heatmap illustrates the correlation of CDRs co-expressed genes with CDRs in ADPC (D) and CRPC (E, F) patient cohorts. (G, H) KEGG pathway analysis (G) and GSEA analysis (H) of enriched biological processes of CDRs and CDRs co-expressed genes. (I, J) The diagram illustrates the working model of CRISPR-Cas13 for RNA silencing and knockdown efficiency of CDRs with the corresponding gRNAs. (K, L) Cell growth assays indicate the impact of CDRs knockdown on the viability of different prostate cancer cells. (M) Western blotting analysis of the expression of cell cycle-regulated genes, including CCND1, CDK1, and p-CDK1, after CDRs knockdown. ∗∗ p < 0.01. CDRs refers to CDC20 (cell division cycle 20), DTL (denticleless E3 ubiquitin protein ligase), and RRM2 (ribonucleotide reductase M2). NE, neuroendocrine; KEGG, Kyoto Encyclopedia of Genes and Genomes; GSEA, gene set enrichment analysis; CCND1, cyclin D1; CDK1, cyclin-dependent kinase 1.

Article Snippet: Three guide RNAs (gRNA) for each target, including RB1, E2F1, CDC20, RRM2, and DTL, were designed, generated, and cloned into CRSIPR-Cas13 corresponding gRNA backbone (Addgene, 109053).

Techniques: Expressing, CRISPR, Knockdown, Western Blot, Ubiquitin Proteomics

Journal: Genes & Diseases

Article Title: Integrative high-throughput studies to develop novel targets and drugs for the treatment of advanced prostate cancer

doi: 10.1016/j.gendis.2025.101732

Figure Lengend Snippet: CDRs were transcriptionally regulated by the RB1/E2F1 axis in prostate cancer. (A) The diagrams show the canonical E2F1 motif location within the promoter of CDRs. (B) ChIP-sequencing E2F1 enrichment peak within the promoter of CDRs. (C) The relative enrichment of E2F1 within the promoter of CDRs was determined using standard ChIP-qPCR. (D) ChIP-sequencing peaks show the relative enrichment of E2F1 in CDRs' promoters after RB1 is known. (E – G) The relative expression of CDRs in CRPC patients with different RB1 deletion status. (H) CDRs expression in patients with RB1 deletion mutations from different prostate cancer cohorts. (I) qRT-PCR detected the relative expression of CDRs after RB1 or E2F1 knockdown with CRISPR-Cas13. ∗∗ p < 0.01, ∗∗∗ p < 0.001, and ∗∗∗∗ p < 0.0001. CDRs refers to CDC20 (cell division cycle 20), DTL (denticleless E3 ubiquitin protein ligase), and RRM2 (ribonucleotide reductase M2). RB1, retinoblastoma tumor suppressor 1; E2F1, early 2 factor 1; ChIP, chromatin immunoprecipitation; qRT-PCR, quantitative real-time PCR.

Article Snippet: Three guide RNAs (gRNA) for each target, including RB1, E2F1, CDC20, RRM2, and DTL, were designed, generated, and cloned into CRSIPR-Cas13 corresponding gRNA backbone (Addgene, 109053).

Techniques: ChIP-sequencing, ChIP-qPCR, Expressing, Quantitative RT-PCR, Knockdown, CRISPR, Ubiquitin Proteomics, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

Journal: Genes & Diseases

Article Title: Integrative high-throughput studies to develop novel targets and drugs for the treatment of advanced prostate cancer

doi: 10.1016/j.gendis.2025.101732

Figure Lengend Snippet: Virtual screening identified compounds that suppressed advanced prostate cancer. (A) The diagram illustrates structure-based virtual screening strategies for CDRs-targeted compounds. (B) The heatmap shows the binding affinity of compounds with CDRs. The red indicated a higher binding affinity of compounds with the corresponding compounds. (C, D) Cell viability assays were used to determine the tumor suppressive effect of compounds with high CDRs-binding affinity in different prostate cancer cell models. (E – G) The 2D structure of Q199, XDD60, and A79, which exhibits the most significant anti-tumor efficacy in prostate cancer cell models. CDRs refers to CDC20 (cell division cycle 20), DTL (denticleless E3 ubiquitin protein ligase), and RRM2 (ribonucleotide reductase M2).

Article Snippet: Three guide RNAs (gRNA) for each target, including RB1, E2F1, CDC20, RRM2, and DTL, were designed, generated, and cloned into CRSIPR-Cas13 corresponding gRNA backbone (Addgene, 109053).

Techniques: Binding Assay, Ubiquitin Proteomics

Journal: Genes & Diseases

Article Title: Integrative high-throughput studies to develop novel targets and drugs for the treatment of advanced prostate cancer

doi: 10.1016/j.gendis.2025.101732

Figure Lengend Snippet: Compounds targeting CDRs exhibited superior anti-tumor efficacy compared with AR antagonists. (A – E) The tumor cell growth inhibition effects of different dosages of Q199, XDD60, and A79, as well as enzalutamide, were determined with CCK-8 assays (A–D), and the IC 50 of each agent was calculated with three independent experiments (E). (F, G) The histograms show the relative cell viability after being treated with 5 M of Q199, XDD60, or A79 alone, or a combination. (H) The Venn diagram shows the overlap of Q199, XDD60, and A79 potential targets predicted with SwissTargetPrediction ( http://swisstargetprediction.ch/ ). Molecular docking shows the binding of CDRs with Q199, XDD60, and A79. (I) The lowest binding (LB) affinity of CDRs with Q199, XDD60, and A79. ns, not significant. ∗∗ p < 0.01. CDRs refers to CDC20 (cell division cycle 20), DTL (denticleless E3 ubiquitin protein ligase), and RRM2 (ribonucleotide reductase M2). AR, androgen receptor.

Article Snippet: Three guide RNAs (gRNA) for each target, including RB1, E2F1, CDC20, RRM2, and DTL, were designed, generated, and cloned into CRSIPR-Cas13 corresponding gRNA backbone (Addgene, 109053).

Techniques: Inhibition, CCK-8 Assay, Binding Assay, Ubiquitin Proteomics

Journal: Advanced Science

Article Title: Icaritin Ameliorates Cisplatin‐Induced Mitochondrial Metabolic Dysfunction‐Associated Nephrotoxicity and Synergistically Potentiates Its Antitumor Efficacy

doi: 10.1002/advs.202506712

Figure Lengend Snippet: Chemoproteomics reveals that cisplatin induces renal toxicity by targeting mitochondrial proteins. A) Overall workflow for the chemoproteomics profiling of potential CDDP‐acting targets in the kidney. B) Protein labeling with CDDP‐P in kidney lysis. C) Proteins with labeled CDDP‐P and CDDP. D) CDDP targeting mitochondrial proteins; Comp group, pre‐incubation with excess CDDP to compete with CDDP‐P bound proteins. E) CETSA‐WB assay to detect CDDP‐bound mitochondrial proteins. F) Fluorescent labeling assay to access CDDP‐bound residues of recombinant PC (Pro36 ~ Glu486), PCCA (Val580 ~ Glu728), MCCC1 (Ala512 ~ Glu725), and SDHC (Met1 ~ Arg72) proteins. G) CDDP‐binding proteins involving in metabolic processes.

Article Snippet: Primary antibodies: NF‐kB p65 (Cat# 10745‐1‐AP), NF‐kB p‐p65 (Cat# 82335‐1‐RR), TNF‐α (Cat# 17590‐1‐AP), IL‐6 (Cat# 21865‐1‐AP), PCCA (Cat# 21988‐1‐AP), PC (Cat# 16588‐1‐AP), MCCC1 (Cat# 14861‐1‐AP) SLC25A5 (Cat# 17796‐1‐AP), ATP5F1C (Cat# 10910‐1‐AP), Histone H3 (Cat#17168‐1‐AP) and β‐actin (Cat# 66009–1‐Ig) were sourced from Proteintech (Chicago, USA).

Techniques: Labeling, Lysis, Incubation, Recombinant, Binding Assay