Journal: Nature Communications

Article Title: Phosphoglycerate dehydrogenase-mediated serine reprogramming aggravates macrophage hyperinflammation in murine Pseudomonas aeruginosa pneumonia

doi: 10.1038/s41467-026-69539-1

Figure Lengend Snippet: a Transcriptional profiling of pro-inflammatory genes and anti-inflammatory genes between si NC and si Phgdh -treated iAMs after PAO1 (MOI = 1) infection for 2 h ( n = 3); b KEGG pathway enrichment analysis of DEGs between si NC and si Phgdh -treated iAMs after PAO1 infection ( n = 3); c Western blot analysis of MAPK signaling pathway (p-ERK/ERK1/2、p-P38/P38、p-JNK/JNK) in lung tissue of DMSO and CBR-5884 treated mice; d Western blot analysis of MAPK signaling pathway in iAMs transfected with si NC or si Phgdh ; e Western blot analysis of MAPK signaling pathway in iBMDMs infected with lentivirus expressing empty vector ( EV ) or Phgdh (OE); f Concentration of serine in lung tissue and iAMs pre-treated with CBR-5884 or si Phgdh after PAO1 infection ( n = 3, means ± SEMs); g Activation of p-ERK1/2 in lung tissue of control- (10 mg/kg serine) and high-serine (50 mg/kg serine) diet-fed mice; h Western blot analysis of p-ERK/ERK1/2 in iAMs transfected with si NC and si Phgdh and treated with or without L-serine (400 μM); i Il6 and Il1b mRNA in iAMs transfected with si NC and si Phgdh and treated with or without L-serine (400 μM) after PAO1 infection ( n = 3, means ± SEMs); j qPCR analysis of Il6 and Il1b mRNA in iAMs 1 h pre-treated with ERK1/2 inhibitor (U0126-Etoh) after stimulation with 0 and 400 μM L-serine ( n = 3, means ± SEMs). An unpaired two-sided Student’s t-test was used in ( f , j ); One-way ANOVA followed by Dunnett’s multiple comparison test in ( i ). All experiments are repeated three times independently and similar results are obtained. Source data are provided as a Source Data file.

Article Snippet: Primary antibodies used in this study include Phgdh (Proteintech, Cat. No. 14719-1-AP, 1:1000), Phospho-p44/42 MAPK (ERK1/2) (Thr202/Tyr204) (CST, Cat. No. 4370 T, 1:1000), p44/42 MAPK (ERK1/2) Antibody (CST, Cat. No. 9102S, 1:1000), Phospho-p38 MAPK (Thr180/Tyr182) Antibody (CST, Cat. No. 9211S, 1:1000), p38 MAPK Antibody (CST, Cat. No. 9212S, 1:1000), p-JNK (Santa, Cat. No. sc-6254, 1:500), JNK (Santa, Cat. No. sc-7345, 1:500), MKP-2/DUSP4 (Proteintech, Cat. No. 14719-1-AP, 1:1000), DUSP2 (Proteintech, Cat. No. 27327-1-AP, 1:1000), Histone H3 (tri methyl K27) (Abcam, Cat. No. ab6002, 1:1000), Histone H3 (Abcam, Cat. No. ab201456, 1:1000), iNOS (Proteintech, Cat. No. 18985-1-AP, 1:2500), Arginase-1 (Proteintech, Cat. No. 16001-1-AP, 1:1000), Recombinant Anti-GAPDH antibody (HRP Conjugated) (Servicebio, Cat. No. ZB15004-HRP-100, 1:2500), β-Actin Antibody (CST, Cat. No. 4967S, 1:1000), and HSP90 alpha/beta (Santa, Cat. No. sc-13119, 1:1000).

Techniques: Infection, Western Blot, Transfection, Expressing, Plasmid Preparation, Concentration Assay, Activation Assay, Control, Comparison

Journal: Nature Communications

Article Title: Phosphoglycerate dehydrogenase-mediated serine reprogramming aggravates macrophage hyperinflammation in murine Pseudomonas aeruginosa pneumonia

doi: 10.1038/s41467-026-69539-1

Figure Lengend Snippet: a Candidate genes that commonly modulate ERK1/2 phosphorylation under both Phgdh knockdown and serine deprivation conditions ( n = 3); b qPCR analysis of the candidate genes (e.g., Dusp1, Dusp2, Dusp3, Dusp4, Dusp5, Dusp9, Dusp10, Spry2, Fgfr1 ) in iAMs derived from Phgdh fl/fl Lyz2 Cre and Phgdh fl/fl mice ( n = 3, means ± SEMs); c Western blot analysis of Dusp2 and Dusp4 in iAMs derived from Phgdh fl/fl Lyz2 Cre and Phgdh fl/fl mice, and iAMs treated with or without L-serine after PAO1 infection; d qPCR analysis of Dusp4, Il6 and Il1b mRNA in iAMs transfected with si NC and si Dusp4 and treated with or without L-serine after PAO1 infection ( n = 3 for serine deprived group, n = 4 for serine treated group, means ± SEMs); e Schematic diagram of 13 C flux in the SSP and one-carbon metabolism, and heatmap of targeted metabolites in iAMs derived from Phgdh fl/fl Lyz2 Cre and Phgdh fl/fl mice after PAO1 infection ( n = 5 for Phgdh fl/fl group, n = 6 for Phgdh fl/fl Lyz2 Cre group); f Distribution of targeted metabolites in iAMs derived from Phgdh fl/fl Lyz2 Cre and Phgdh fl/fl mice after PAO1 infection ( n = 5 for Phgdh fl/fl group, n = 6 for Phgdh fl/fl Lyz2 Cre group, means ± SEMs); g Distribution of 13 C labels metabolites in iAMs derived from Phgdh fl/fl Lyz2 Cre and Phgdh fl/fl mice after PAO1 infection ( n = 4 for the 13 C labeled Phgdh fl/fl group, n = 5 for the 13 C labeled Phgdh fl/fl Lyz2 Cre group, means ± SEMs); h Western blot analysis of H3K27me3 in iAMs derived from Phgdh fl/fl Lyz2 Cre and Phgdh fl/fl mice, and iAMs treated with or without L-serine after PAO1 infection; i ChIP-qPCR analysis of the binding of H3K27me3 to the Dusp4 promoter regions in iAMs derived from Phgdh fl/fl Lyz2 Cre and Phgdh fl/fl mice with primers targeting distinct sites ( n = 4, means ± SEMs); j ChIP-qPCR analysis of H3K27me3 enrichment at the Dusp4 promoters in uninfected and PAO1 infected iAMs derived from Phgdh fl/fl Lyz2 Cre and Phgdh fl/fl mice ( n = 3, means ± SEMs); k ChIP-qPCR analysis of H3K27me3 enrichment at the Dusp4 promoters in iAMs cultured with vehicle, serine (400 μM) or SAM (200 μM) ( n = 3, means ± SEMs). An unpaired, two-tailed Student’s t-test was used in ( b , f , g ); One-way ANOVA followed by Dunnett’s multiple comparison test in ( d , k ). All experiments are repeated three times independently and similar results are obtained. Source data are provided as a Source Data file.

Article Snippet: Primary antibodies used in this study include Phgdh (Proteintech, Cat. No. 14719-1-AP, 1:1000), Phospho-p44/42 MAPK (ERK1/2) (Thr202/Tyr204) (CST, Cat. No. 4370 T, 1:1000), p44/42 MAPK (ERK1/2) Antibody (CST, Cat. No. 9102S, 1:1000), Phospho-p38 MAPK (Thr180/Tyr182) Antibody (CST, Cat. No. 9211S, 1:1000), p38 MAPK Antibody (CST, Cat. No. 9212S, 1:1000), p-JNK (Santa, Cat. No. sc-6254, 1:500), JNK (Santa, Cat. No. sc-7345, 1:500), MKP-2/DUSP4 (Proteintech, Cat. No. 14719-1-AP, 1:1000), DUSP2 (Proteintech, Cat. No. 27327-1-AP, 1:1000), Histone H3 (tri methyl K27) (Abcam, Cat. No. ab6002, 1:1000), Histone H3 (Abcam, Cat. No. ab201456, 1:1000), iNOS (Proteintech, Cat. No. 18985-1-AP, 1:2500), Arginase-1 (Proteintech, Cat. No. 16001-1-AP, 1:1000), Recombinant Anti-GAPDH antibody (HRP Conjugated) (Servicebio, Cat. No. ZB15004-HRP-100, 1:2500), β-Actin Antibody (CST, Cat. No. 4967S, 1:1000), and HSP90 alpha/beta (Santa, Cat. No. sc-13119, 1:1000).

Techniques: Phospho-proteomics, Knockdown, Derivative Assay, Western Blot, Infection, Transfection, Labeling, ChIP-qPCR, Binding Assay, Cell Culture, Two Tailed Test, Comparison

Journal: Cell Cycle

Article Title: Exosomes derived from AHR-overexpressing human umbilical cord mesenchymal stem cells attenuate H/R injury via AHR/NLRP3 pathway

doi: 10.1080/15384101.2025.2609649

Figure Lengend Snippet: hUC-MSCs Regulate Myocardial Protection through the AHR/NLRP3 Signaling Pathway. Western blot (A) and qPCR (B) analysis of NLRP3, Bax, NF-κB, caspase-1, AHR, CYP1A1, and CYP1A2 protein and mRNA expression in myocardial cells (biological replicates, n = 3). (C) ELISA detection of inflammatory cytokine levels in the culture supernatant (biological replicates, n = 6). Western blot (D) and qPCR (E) analysis of AHR protein and mRNA expression in hUC-MSCs (biological replicates, n = 3). Groups: AC16 (AC16 cells cultured under normal conditions); AC16-H/R (AC16 cells subjected to hypoxia/reoxygenation); hUC-MSCs+AC16-H/R (co-culture of AC16 (lower chamber) and hUC-MSCs (upper chamber)); hUC-MSCs+AC16-H/R (co-culture of AC16-H/R (lower chamber) and hUC-MSCs (upper chamber)). “**” indicates p < 0.01; “***” indicates p < 0.001.

Article Snippet: NLRP3 Rabbit mAb (D4D8T, Cat. No. 15,101), Cleaved Caspase-1 Rabbit mAb (D57A2, Cat. No. 4199), Bax Antibody (Cat. No. 2772), AHR Rabbit mAb (D5S6H, Cat. No. 83,200), CYP1A2 Mouse mAb (D2V7S, Cat. No. 14,719), CD81 Rabbit mAb (D3N2D, Cat. No. 56,039), Calnexin Antibody (Cat. No. 2433), and GAPDH Rabbit mAb (14C10, Cat. No. 2118) were purchased from Cell Signaling Technology (Danvers, MA, USA).

Techniques: Western Blot, Expressing, Enzyme-linked Immunosorbent Assay, Cell Culture, Co-Culture Assay

Journal: Cell Cycle

Article Title: Exosomes derived from AHR-overexpressing human umbilical cord mesenchymal stem cells attenuate H/R injury via AHR/NLRP3 pathway

doi: 10.1080/15384101.2025.2609649

Figure Lengend Snippet: hUC-MSCs-AHR-exo Suppress Inflammatory Signaling in DC – T Cell Co-cultures. (A) Western blot analysis of NLRP3, caspase-1, NF-κB, and AHR-related proteins (AHR, CYP1A1, CYP1A2) in co-cultured DCs and T cells (biological replicates, n = 3). (B) ELISA detection of cytokine levels in the supernatant, showing reduced IL-1β, TNF-α, IL-18 and increased IL-10, TGF-β after AHR-exo treatment. Model: LPS-induced DC and T cell co-culture model. DC cells and T cells were co-cultured in direct contact (biological replicates, n = 6). “**” indicates p < 0.01; “***” indicates p < 0.001.

Article Snippet: NLRP3 Rabbit mAb (D4D8T, Cat. No. 15,101), Cleaved Caspase-1 Rabbit mAb (D57A2, Cat. No. 4199), Bax Antibody (Cat. No. 2772), AHR Rabbit mAb (D5S6H, Cat. No. 83,200), CYP1A2 Mouse mAb (D2V7S, Cat. No. 14,719), CD81 Rabbit mAb (D3N2D, Cat. No. 56,039), Calnexin Antibody (Cat. No. 2433), and GAPDH Rabbit mAb (14C10, Cat. No. 2118) were purchased from Cell Signaling Technology (Danvers, MA, USA).

Techniques: Western Blot, Cell Culture, Enzyme-linked Immunosorbent Assay, Co-Culture Assay