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: Nature Communications

Article Title: Leucine regulates autophagy via acetylation of the mTORC1 component raptor

doi: 10.1038/s41467-020-16886-2

Figure Lengend Snippet: a Leu metabolic pathway. Red box shows MCCC1 gene. b Autophagy activation by MCCC1 depletion. siRNA knockdown of MCCC1 in HeLa cells was used to determine whether MCCC1 can regulate autophagy (Con; scrambled, nontargeting siRNA, MCCC1; SMARTpool MCCC1 targeted siRNA). Blots are representative of four independent experiments ( N = 4). Two-tailed unpaired t -test. c Immunostaining of HeLa cells treated with MCCC1 SMARTpool siRNA using MCCC1 (red) and LC3 (green) antibodies, nuclei are stained with DAPI (blue). # MCCC1 knockdown cells, *non-knockdown cells. Scale bar, 10 μm. N = 4; 70–80 cells scored per condition per experiment. Two-tailed unpaired t -test. d Reduced HTT (Q74) aggregation in MCCC1 knockdown HeLa cells. HeLa cells were seeded on coverslips in triplicates, transfected with siRNAs targeting control or MCCC1, followed by HA-tagged HTT (Q74) expression. N = 4, 40–60 cells scored per condition per experiment. Two-tailed unpaired t -test. e α-synuclein degradation assay in control or MCCC1 knockdown ATG16L1 WT or CRISPR KO HeLa cells. Cells were transfected with control or MCCC1 siRNAs for 3 days. In the last 24 h, cells were transfected with empty pEGFP (as a “transfection/loading control”) + pEGFP-α-synuclein A53T. Levels of α-synuclein A53T are expressed as a ratio to GFP. N = 3. * p < 0.05 vs. control cells; two-tailed unpaired t -test. Autophagy activation by MCCC1 depletion in SH-SY5Y cells ( f ) and primary neurons ( g ). N = 3. *** p < 0.001 vs. control cells; two-tailed unpaired t -test. Long exposure (LE); Short exposure (SE). h Autophagic flux in mouse primary cortical neurons from mRFP-GFP-LC3 (tfLC3) transgenic mice. Representative confocal z-stack images (right panel) and total number of GFP/mRFP dots (autophagosomes) and mRFP-only dots (autolysosomes). In total, 25–35 cells analyzed per condition per experiment; two-tailed unpaired t -test. Scale bar, 10 μm. Data are presented as mean values ± SEM. Source data are provided as a file.

Article Snippet: The following DNA or siRNA/shRNA constructs were also used in this work: empty pEGFP (Clontech), pEGFP-α-synuclein A53T and pcDNA3.1-myc-6XHis (Invitrogen); pCMV6-XL5-MCCC1 (#SC113201) from Origene; pcDNA3.1-EP300-6XHis (#23252), pRK5-HA-YFP-raptor (#73385), pRK5-HA-raptor (#8513), pcDNA4-BECN1-Flag (#24388) from Addgene.

Techniques: Activation Assay, Two Tailed Test, Immunostaining, Staining, Transfection, Expressing, Degradation Assay, CRISPR, Transgenic Assay

Journal: Nature Communications

Article Title: Leucine regulates autophagy via acetylation of the mTORC1 component raptor

doi: 10.1038/s41467-020-16886-2

Figure Lengend Snippet: a mTORC1 inhibition in MCCC1-depleted cells. HeLa cells were treated with MCCC1 siRNA and immunostained for MCCC1 (green) and phosphorylated S6 (red), nuclei were stained with DAPI (blue). For ease of visualization, the cell outlines are highlighted in white dashed lines. # MCCC1 knockdown cells, *non-knockdown cells. Scale bar, 10 μm. N = 4, 30–40 cells scored per condition per experiment. Two-tailed unpaired t -test. The effect of mTOR inhibitor Torin1 in MCCC1 knockdown HeLa ( b ) or SH-SY5Y ( c ) and Mccc1 knockdown primary neurons ( d ). Control and MCCC1 knockdown cells were treated with 0.5 µM Torin1 (or DMSO) for 4 h. N = 4 for HeLa cells or N = 3 for SH-SY5Y and primary neurons. *** p < 0.001 vs. control cells; two-tailed unpaired t -test. e Autophagy response to changes in Leu levels. HeLa cells were treated with scrambled siRNA or MCCC1 siRNA then incubated in Leu-depleted media for 4 h or incubated in Leu-depleted media for 4 h, followed by the re-addition of 10 µM of Leu to the media for 1 h. N = 3, 50–60 cells scored per condition per experiment. Two-tailed unpaired t -test. f Increased number of WIPI2 dots in Leu-depleted media. N = 3, 40 cells scored per condition per experiment. Scale bar, 5 μm. Two-tailed unpaired t -test. g Rescue of autophagy and mTORC1 activation in MCCC1 knockdown by dichloroacetate (DCA), not Leu or KIC. MCCC1 knockdown HeLa cells were treated with 10 µM Leu, 10 mM KIC, or 10 mM DCA for 1 h. N = 3. Two-tailed unpaired t -test. Data are presented as mean values ± SEM. Source data are provided as a file.

Article Snippet: The following DNA or siRNA/shRNA constructs were also used in this work: empty pEGFP (Clontech), pEGFP-α-synuclein A53T and pcDNA3.1-myc-6XHis (Invitrogen); pCMV6-XL5-MCCC1 (#SC113201) from Origene; pcDNA3.1-EP300-6XHis (#23252), pRK5-HA-YFP-raptor (#73385), pRK5-HA-raptor (#8513), pcDNA4-BECN1-Flag (#24388) from Addgene.

Techniques: Inhibition, Staining, Two Tailed Test, Incubation, Activation Assay

Journal: Nature Communications

Article Title: Leucine regulates autophagy via acetylation of the mTORC1 component raptor

doi: 10.1038/s41467-020-16886-2

Figure Lengend Snippet: a AcCoA levels were assessed using the PicoProbe AcCoA assay kit. HeLa cells were incubated in nutrient-depleted conditions for 4 h followed by lysis and measurement of AcCoA levels. N = 4. Two-tailed unpaired t -test. b Effect of DCA and Leu on mTOR signaling and autophagy modulation caused by MCCC1 knockdown. Control cells, and cells treated with MCCC1 siRNA were treated with 10 mM DCA or 10 µM Leu for 1 h. Cells were lysed and western blots for phosphorylated S6K1 (p-S6K1) and total S6K1, as well as LC3 and MCCC1 are shown. N = 3. Two-tailed unpaired t -test. c Rescue of activated autophagy in MCCC1-depleted cells by DCA. 10 mM DCA for 1 h treatment restored the increased LC3 dots in MCCC1-depleted cells. N = 3, 60–70 cells scored per condition per experiment. Two-tailed unpaired t -test. Scale bar, 10 μm. AcCoA-induced autophagy regulation in mTORC1-dependent manner. Treatment with 0.5 µM Torin1 for 4 h or RRAGA and RRAGB double-knockdown (RRAGA + B) blocked the rescue effect of Leu or DCA on autophagy activation (LC3-II level ( d ) and LC3 dots ( e )) by Leu depletion. HeLa cells were treated with scrambled siRNA or MCCC1 siRNA then incubated in Leu-depleted media for 4 h or incubated in Leu-depleted media for 4 h, followed by the re-addition of 10 µM of Leu or 10 mM DCA to the media for 1 h. N = 3, 40–50 cells scored per condition per experiment. Two-way ANOVA with post-hoc Tukey’s multiple comparison test. Scale bar, 10 μm. Data are presented as mean values ± SEM. Source data are provided as a file.

Article Snippet: The following DNA or siRNA/shRNA constructs were also used in this work: empty pEGFP (Clontech), pEGFP-α-synuclein A53T and pcDNA3.1-myc-6XHis (Invitrogen); pCMV6-XL5-MCCC1 (#SC113201) from Origene; pcDNA3.1-EP300-6XHis (#23252), pRK5-HA-YFP-raptor (#73385), pRK5-HA-raptor (#8513), pcDNA4-BECN1-Flag (#24388) from Addgene.

Techniques: Incubation, Lysis, Two Tailed Test, Western Blot, Activation Assay

Journal: Nature Communications

Article Title: Leucine regulates autophagy via acetylation of the mTORC1 component raptor

doi: 10.1038/s41467-020-16886-2

Figure Lengend Snippet: a HeLa cells were treated with control siRNA or MCCC1 siRNAs, and cytosolic EP300 activity was assessed. N = 4. Two-tailed unpaired t -test. b Reduced raptor acetylation in MCCC1 knockdown cells. HeLa cells were treated with control or MCCC1 siRNA and transfected with HA-raptor. Following incubation in Leu-depleted media for 4 h, cells were lysed and raptor was immunoprecipitated using an anti-HA antibody. N = 4. c HeLa cells were depleted of raptor with siRNA and transfected with cDNA constructs encoding either raptor WT or raptor K1097R mutant (KR) (both HA-tagged). N = 4. d mTORC1 activity (phosphorylated S6) and LC3 dot numbers in HeLa cells expressing raptor WT or raptor KR. *HA-raptor WT or KR-expressing cells, # nontransfected cells. Scale bar, 10 μm. N = 3, 20–30 cells scored per condition per experiment. Two-tailed unpaired t -test. Acetylated PIK3C3 ( e ) and BECN1 levels ( f ) in HeLa cells depleted of raptor then reconstituted with raptor WT or raptor KR. Two-tailed unpaired t -test. HC, heavy chain. N = 4. g Effects of EP300 activator on mTORC1 signaling and autophagy in response to Leu deprivation with or without DCA in HeLa cells depleted of raptor then reconstituted with raptor WT or raptor KR. HeLa cells were incubated in Leu-depleted media for 4 h or incubated in Leu-depleted media with Torin1 for 4 h, followed by re-addition of 10 mM DCA to the media for 1 h. 50 µM CTB for 12 h was used to activate EP300. Blots are representative of three biologically independent experiments ( N = 3). h Leu abundance regulates autophagy in many cell types via its metabolite AcCoA. AcCoA activates EP300, which acetylates raptor, leading to mTORC1 activation, which inhibits autophagy. In Leu deprivation conditions, autophagy activation is mainly mediated by decreased raptor acetylation causing mTORC1 inhibition, rather than by altered acetylation of other autophagy regulators. Data are presented as mean values ± SEM. Source data are in file.

Article Snippet: The following DNA or siRNA/shRNA constructs were also used in this work: empty pEGFP (Clontech), pEGFP-α-synuclein A53T and pcDNA3.1-myc-6XHis (Invitrogen); pCMV6-XL5-MCCC1 (#SC113201) from Origene; pcDNA3.1-EP300-6XHis (#23252), pRK5-HA-YFP-raptor (#73385), pRK5-HA-raptor (#8513), pcDNA4-BECN1-Flag (#24388) from Addgene.

Techniques: Activity Assay, Two Tailed Test, Transfection, Incubation, Immunoprecipitation, Construct, Mutagenesis, Expressing, Activation Assay, Inhibition