Journal: International Journal of Molecular Medicine

Article Title: Triptolide exerts antiviral effects and alleviates influenza A-induced pneumonia by inhibiting the overactivation of absent in melanoma 2 signaling in immune cells

doi: 10.3892/ijmm.2026.5829

Figure Lengend Snippet: H1N1 infection affects cell viability, inflammatory cytokine secretion and interactions between HBEpiCs and THP-1 cells. (A) CCK-8 assay revealed that HBEpiC viability decreased in a concentration-dependent manner following H1N1 infection. (B) ELISA revealed that the levels of IL-1β, IL-6, TNF-α, and IL-8 in HBEpiCs decreased with increasing H1N1 infection. (C) CCK-8 assay indicated that supernatants from H1N1-infected HBEpiC cultures reduced the viability of THP-1 cells in a dose-dependent manner. (D) ELISA results suggested that the levels of inflammatory cytokines (IL-1β, IL-6, TNF-α and IL-8) in THP-1 cells were decreased following exposure to supernatants from H1N1-infected HBEpiC cultures. (E) Cell adhesion assay revealed that the number of THP-1 cells adhering to HBEpiCs increased with increasing H1N1 concentration (scale bar, 10 μ m). Arrow indicates THP-1 cells that remain attached to the surface of HBEpiCs, highlighting the adhesion interaction between the two cell types. (F) Transwell assay suggested that H1N1 infection enhanced the migration capacity of THP-1 cells, with increased migration observed at higher virus concentrations (scale bar, 50 μ m). The data are presented as the mean ± standard deviation; ** P<0.01, *** P<0.001 vs. control. H1N1, influenza A; HBEpiCs, human bronchial epithelial cells; ELISA, enzyme-linked immunosorbent assay; IL, interleukin; TNF-α, tumor necrosis factor-α; Con, control; MOI, multiplicity of infection.

Article Snippet: Cell supernatants were collected and analyzed using Human TNF-α High Sensitivity ELISA Kit [cat. no. EK182HS; Hangzhou Multi Sciences (Lianke) Biotech Co., Ltd.], Human IL-8 ELISA Kit [cat. no. EK108; Hangzhou Multi Sciences (Lianke) Biotech Co., Ltd.], a human IL-1β ELISA kit [EH0185; Hangzhou Multi Sciences (Lianke) Biotech Co., Ltd.] and IL-6 [cat. no. EK1217; Hangzhou Multi Sciences (Lianke) Biotech Co., Ltd.] according to the manufacturer's instructions.

Techniques: Infection, CCK-8 Assay, Concentration Assay, Enzyme-linked Immunosorbent Assay, Cell Adhesion Assay, Transwell Assay, Migration, Virus, Standard Deviation, Control

Journal: International Journal of Molecular Medicine

Article Title: Triptolide exerts antiviral effects and alleviates influenza A-induced pneumonia by inhibiting the overactivation of absent in melanoma 2 signaling in immune cells

doi: 10.3892/ijmm.2026.5829

Figure Lengend Snippet: TP modulates the inflammatory response and immune cell activity in H1N1-infected HBEpiCs and THP-1 cells. (A) No significant changes were observed in HBEpiCs treated with various concentrations of TP (5, 10 and 20 nM) following H1N1 infection compared with the control. (B) After TP treatment, the levels of the inflammatory cytokines IL-1β, IL-6, TNF-α and IL-8 in HBEpiCs were markedly lower than those in the untreated group. (C) The viability of THP-1 cells pretreated with H1N1-infected HBEpiC culture supernatant decreased after TP treatment. (D) The levels of IL-1β, IL-6, TNF-α, and IL-8 in THP-1 cells were markedly lower after TP treatment. (E) The adhesion of THP-1 cells to HBEpiCs induced by H1N1 infection decreased in a dose-dependent manner with increasing TP concentration (scale bar, 10 μ m). Arrow indicates THP-1 cells that remain attached to the surface of HBEpiCs, highlighting the adhesion interaction between the two cell types. (F) The migration capacity of THP-1 cells was markedly reduced when the supernatant from H1N1-infected HBEpiC cultures was treated with TP (scale bar, 50 μ m). The data are presented as the mean ± standard deviation; * P<0.05, ** P<0.01, *** P<0.001 vs. control. TP, triptolide; H1N1, influenza A; HBEpiCs, human bronchial epithelial cells; IL, interleukin; TNF-α, tumor necrosis factor-α; Con, control.

Article Snippet: Cell supernatants were collected and analyzed using Human TNF-α High Sensitivity ELISA Kit [cat. no. EK182HS; Hangzhou Multi Sciences (Lianke) Biotech Co., Ltd.], Human IL-8 ELISA Kit [cat. no. EK108; Hangzhou Multi Sciences (Lianke) Biotech Co., Ltd.], a human IL-1β ELISA kit [EH0185; Hangzhou Multi Sciences (Lianke) Biotech Co., Ltd.] and IL-6 [cat. no. EK1217; Hangzhou Multi Sciences (Lianke) Biotech Co., Ltd.] according to the manufacturer's instructions.

Techniques: Activity Assay, Infection, Control, Concentration Assay, Migration, Standard Deviation

Journal: iScience

Article Title: 3-Hydroxypropionic acid converts inflammatory macrophage glycolysis into mitochondrial oxidation through GAPDH carboxyethylation

doi: 10.1016/j.isci.2026.116258

Figure Lengend Snippet: 3-HPA inhibits the secretion of inflammatory factors and glycolysis in macrophages (A and B) Schematic diagram of THP-1 cell (A) and BMDMs (B) activation into pro-inflammatory macrophages. Created with BioRender.com. (C) The concentrations of IL-6, TNF-α, and IL-1β in THP-1 cell supernatants were quantified by ELISA after 24 h treatment with LPS (100 ng/mL), or LPS+3-HPA (5 mM). Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, and ∗∗∗∗p < 0.0001. (D) The concentrations of IL-6, TNF-α, and IL-1β in supernatants of THP-1 cells treated with different concentrations of 3-HPA (0, 0.625, 1.25, 5 mM) followed by LPS stimulation. Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Dunnett’s multiple comparisons test ∗p < 0.05, ∗∗p < 0.01, and ∗∗∗p < 0.001. (E) The concentrations of IL-6, TNF-α, and IL-1β in BMDM cell supernatants were quantified by ELISA after 24 h treatment with LPS (100 ng/mL) or LPS+3-HPA (5 mM). Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, and ∗∗∗∗p < 0.0001. (F) Bubble plot of KEGG pathway enrichment analysis for differentially expressed genes between LPS (100 ng/mL) and LPS+3-HPA (5 mM) treated in THP-1 cells. The size of each bubble represents the number of differentially expressed genes, and the color indicates the enrichment factor. (G and H) Pyruvate and lactate levels in THP-1 cells (G) and BMDMs (H) treated with LPS (100 ng/mL), or LPS+3-HPA (5 mM). (I) Immunoblots of protein expression levels of HK, GAPDH, PKM, and LDHA in THP-1 cells treated with LPS (100 ng/mL), or LPS+3-HPA (5 mM), and quantitative results of GAPDH. (J) The mRNA levels of GAPDH in THP-1 cells treated with LPS (100 ng/mL) or LPS+3-HPA (5 mM). (K) GAPDH activity assay in THP-1 cells and BMDMs treated with PBS, LPS (100 ng/mL), or LPS+3-HPA (5 mM). Data in (G–K) are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, and ∗∗∗∗p < 0.0001; ns, not significant.

Article Snippet: Human IL-1β Precoated ELISA Kit , Dakewe , 1110122.

Techniques: Activation Assay, Enzyme-linked Immunosorbent Assay, Western Blot, Expressing, Activity Assay

Journal: iScience

Article Title: 3-Hydroxypropionic acid converts inflammatory macrophage glycolysis into mitochondrial oxidation through GAPDH carboxyethylation

doi: 10.1016/j.isci.2026.116258

Figure Lengend Snippet: 3-HPA enhances the metabolite content of the TCA cycle and mitochondrial oxidation (A) Schematic diagram of THP-1 with 2-DG treatment. Created with BioRender.com. (B) Concentrations of IL-6, TNF-α, and IL-1β in supernatants of THP-1 cells treated with LPS, LPS+3-HPA, LPS+2-DG, or LPS+3-HPA+2-DG. Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, and ∗∗∗∗p < 0.0001; ns, not significant. (C) Schematic diagram of THP-1 with high glucose treatment. Created with BioRender.com. (D) Concentrations of IL-6, TNF-α, and IL-1β in supernatants of THP-1 cells treated with LPS+3-HPA, LPS+3-HPA+glucose. Data are the means ± SD and n = 3 per group. Statistical significance was determined using unpaired Student’s t test with ∗∗∗p < 0.001; ns, not significant. (E) KEGG pathway enrichment analysis of metabolic pathways in BMDM cells treated with LPS or LPS+3-HPA. (F) Relative abundance of metabolite (ornithine, citrulline, L-malate, succinic acid, trans-aconitic acid, cis-aconitic acid) in BMDM cells treated with LPS or LPS+3-HPA. Data are the means ± SD and n = 4 per group. Statistical significance was determined using unpaired Student’s t test with ∗p < 0.05; ∗∗p < 0.01. (G) Correlation network of metabolites and genes in the metabolic pathway. Nodes represent metabolites (blue squares) and genes (colored circles). Gray edges indicate pairwise correlations between metabolites and genes. The colors similarly represent expression levels, with red typically indicating higher expression and blue indicating lower expression compared to the mean. (H) Schematic diagram of arginine metabolism and the TCA cycle. (I) Heatmap of mitochondrial oxidation-related gene expression associated with differentially expressed metabolites. Red indicates relatively high gene expression, while blue indicates relatively low gene expression within each row. (J) Schematic diagram of the catalytic function of the GAPDH enzyme. (K) Concentrations of the NAD + /NADH ratio in THP-1 cells and BMDM cells treated with PBS, LPS, or LPS+3-HPA. Data are the means ± SD and n = 4 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗∗ p < 0.0001; (L) ATP concentrations in THP-1 cells and BMDMs treated with PBS, LPS, or LPS+3-HPA. Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗ p < 0.05; ∗∗∗∗ p < 0.0001; ns, not significant. (M) Representative images and mitochondrial analysis of BMDM cells treated with PBS, LPS, or LPS+3-HPA. Scale bars, 1 μm (upper) and 0.25 μm (lower). For mitochondrial number, n = 8–12 ( n = 12 for PBS, n = 8 for LPS, n = 9 for LPS+3-HPA group).

Article Snippet: Human IL-1β Precoated ELISA Kit , Dakewe , 1110122.

Techniques: Expressing, Gene Expression

Journal: iScience

Article Title: 3-Hydroxypropionic acid converts inflammatory macrophage glycolysis into mitochondrial oxidation through GAPDH carboxyethylation

doi: 10.1016/j.isci.2026.116258

Figure Lengend Snippet: GAPDH carboxyethylation inhibited macrophage glycolysis and the release of inflammatory factors (A) Schematic workflow illustrating the strategy of silencing endogenous GAPDH via 3′UTR-targeting siRNA and overexpressing exogenous GAPDH. (B) Immunoblot and quantitative analysis of GAPDH protein in 293 T cells transfected with GAPDH 3′UTR-targeting siRNAs (siGAPDH 1, siGAPDH 2) or siRNA NC. Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Dunnett’s multiple comparisons test ∗∗p < 0.01. (C) Relative mRNA expression of GAPDH in 293 T cells transfected with GAPDH 3′UTR-targeting siRNAs (siGAPDH 1, siGAPDH 2) or siRNA NC. Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Dunnett’s multiple comparisons test ∗∗∗∗p < 0.0001. (D) Immunoblot analysis of FLAG-tagged exogenous GAPDH(E) and GAPDH in 293 T cells. Knockdown of endogenous GAPDH with siRNA followed by the overexpression of GAPDH (E). Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Dunnett’s multiple comparisons test with ∗p < 0.05; ns, not significant. (E) Relative mRNA expression of GAPDH in 293 T cells knockdowned endogenous GAPDH (siGAPDH) and overexpressed GAPDH (C) and GAPDH (E), respectively. Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗∗p < 0.01; ∗∗∗p < 0.001; ns, not significant. (F) GAPDH activity assay in 293 T cells transfected with GAPDH 3′UTR siRNA, and overexpressing GAPDH(C), GAPDH(E). Data are the means ± SD and n = 4 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗p < 0.05; ∗∗∗∗p < 0.0001; ns, not significant. (G) Concentrations of lactate and pyruvate in 293 T cells transfected with GAPDH 3′UTR siRNA, and overexpressing GAPDH(C), GAPDH(E). Data are the means ± SD and n = 4 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗p < 0.05, ∗∗p < 0.01, and ∗∗∗∗p < 0.0001. (H) Relative mRNA expression of IL-6 , TNF-α , and IL-1β in THP-1 cells which transfected with GAPDH 3′UTR siRNA, and overexpressing GAPDH(C) or GAPDH(E). Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001; ns, not significant. (I) The concentration of TNF-α in THP-1 cells that overexpressed GAPDH(C) or GAPDH(E). Data are the means ± SD and n = 3 per group. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test with ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001; ns, not significant.

Article Snippet: Human IL-1β Precoated ELISA Kit , Dakewe , 1110122.

Techniques: Western Blot, Transfection, Expressing, Knockdown, Over Expression, Activity Assay, Concentration Assay

Journal: bioRxiv

Article Title: Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

doi: 10.64898/2026.05.03.722406

Figure Lengend Snippet: (A) Schematic of the primary mouse astrocyte cultures. (B) Representative immunofluorescence images of cultured astrocytes stained for GFAP, showing characteristic astrocyte morphology. (C) Overview of RNA-seq and capped small (cs)RNA-seq data generation from astrocytes. The schematic shows the typical distribution of csRNA-seq and RNA-seq at various genomic locations, which allows the identification of Transcriptional Start Site (TSSs) using HOMER2. (D) Volcano plot of RNA-seq differential expression in astrocytes treated with vehicle (Veh) or IL-1B (10 ng/mL, 1 h). (E) Pathway enrichment analysis of IL-1B-induced differentially expressed genes. (F) RT-qPCR validation of selected IL-1B-responsive genes in astrocytes

Article Snippet: Two days before collection, the astrocytes were plated at a density of 500,000 cells per well on 4-well chamber slides to perform immunocytochemistry or a density of 5.5 million cells per 15 cm dish to be treated with 10ng/mL of recombinant human interleukin 1 beta (IL-1B) (Invivogen, Cat#rcyec-h) for 1hr before sample collection.

Techniques: Immunofluorescence, Cell Culture, Staining, RNA Sequencing, Quantitative Proteomics, Quantitative RT-PCR, Biomarker Discovery

Journal: bioRxiv

Article Title: Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

doi: 10.64898/2026.05.03.722406

Figure Lengend Snippet: Genome browser views showing RNA-seq signal at the Cxcl1, Ccl20, Csf2 , and Il6 loci in astrocytes treated with vehicle or IL-1B. These representative examples illustrate the robust transcriptional induction of canonical inflammatory genes following IL-1B stimulation. Gene models and genomic coordinates are shown in mm10 .

Article Snippet: Two days before collection, the astrocytes were plated at a density of 500,000 cells per well on 4-well chamber slides to perform immunocytochemistry or a density of 5.5 million cells per 15 cm dish to be treated with 10ng/mL of recombinant human interleukin 1 beta (IL-1B) (Invivogen, Cat#rcyec-h) for 1hr before sample collection.

Techniques: RNA Sequencing

Journal: bioRxiv

Article Title: Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

doi: 10.64898/2026.05.03.722406

Figure Lengend Snippet: (A) Pairwise correlation analysis of csRNA-seq replicates from untreated and IL-1B-treated astrocytes. (B) Distribution of strand-specific csRNA-seq reads around GENCODE-annotated TSSs, showing strong enrichment at annotated transcriptional start sites. (C) Genomic annotation of astrocytes TSRs, partitioned across promoter, intronic, intergenic, and other genomic features. (D) Average chromatin profiles at promoter-distal TSRs, showing ATAC-seq and H3K27ac enrichment around transcribed regulatory elements. (E) Average csRNA-seq signal centered on promoter-distal ATAC-seq peaks, comparing transcribed and non-transcribed accessible regions (No Tx: 225,150 peaks, Tx: 14,836 peaks). (F) Average mCH profiles at promoter-proximal TSRs, promoter-distal transcribed TSRs, and non-transcribed distal accessible regions in astrocytes (data from ). (G) Distribution of NFIA and TEAD4 ChIP-seq peaks found overlapping TSRs and ATAC-seq peaks in astrocytes. (H)ChIP-seq read density for NFIA and TEAD4 centered on csRNA-seq defined TSRs, showing transcription factor binding immediately upstream of the primary TSS.

Article Snippet: Two days before collection, the astrocytes were plated at a density of 500,000 cells per well on 4-well chamber slides to perform immunocytochemistry or a density of 5.5 million cells per 15 cm dish to be treated with 10ng/mL of recombinant human interleukin 1 beta (IL-1B) (Invivogen, Cat#rcyec-h) for 1hr before sample collection.

Techniques: ChIP-sequencing, Binding Assay

Journal: bioRxiv

Article Title: Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

doi: 10.64898/2026.05.03.722406

Figure Lengend Snippet: (A)Volcano plot of differentially regulated csRNA-seq signal at astrocyte TSRs following IL-1B stimulation, identifying induced and repressed regulatory elements. (B) Genome browser tracks depicting induction of promoter and distal regulatory enhancer transcription by csRNA-seq at the Ccl2 locus. (C) GREAT functional enrichment analysis of IL-1B induced TSRs. (D) Spatial clustering of IL-1B induced TSRs, depicting the density of TSRs in each category adjacent to Induced TSRs. (E) De novo motif enrichment analysis of IL-1B induced TSRs by HOMER. (F) Average csRNA-seq signal centered on promoter-distal NF-κB/p65 peaks, showing increased bidirectional transcription at p65-bound distal elements after IL-1B stimulation, consistent with eRNA induction. (G) Spatial density of NF-κB, AP1, and IRF motifs relative to TSRs (TF binding sites per bp per TSS), showing upstream enrichment of these motifs at IL-1B-induced TSRs compared with unchanged or repressed TSRs.

Article Snippet: Two days before collection, the astrocytes were plated at a density of 500,000 cells per well on 4-well chamber slides to perform immunocytochemistry or a density of 5.5 million cells per 15 cm dish to be treated with 10ng/mL of recombinant human interleukin 1 beta (IL-1B) (Invivogen, Cat#rcyec-h) for 1hr before sample collection.

Techniques: Functional Assay, Binding Assay

Journal: bioRxiv

Article Title: Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

doi: 10.64898/2026.05.03.722406

Figure Lengend Snippet: (A) Genome browser example of an IL-1B-induced locus (Cxcl10) in astrocytes, showing increased transcription initiation after stimulation. (B) Scatter plot comparing IL-1B-induced Log2 csRNA-seq changes at the promoter vs. RNA-seq changes across genes, highlighting genes regulated primarily at initiation (along x-axis) versus those showing stronger changes at the mRNA level (along y-axis). (C) Genome browser tracks at the Junb locus showing increased gene expression and RNAPII elongation in the gene body with limited change in promoter initiation and RNAPII promoter levels, consistent with regulation being mediated primarily at the level of transcription elongation rather than increased initiation. (D) RNAPII ChIP-seq levels at the promoters of IL-1B induced genes stratified by genes with minimal versus strong increases in csRNA-seq initiation activity. (E) Scatter plot comparing changes in overall TSR levels (Log2 Fold change, NT vs. IL-1B) versus their WIP score significance (the −Log10 p-value), identifying TSRs with altered initiation patterns independent of changes in total transcriptional output. (F) Representative examples of TSRs exhibiting a strong change in initiation pattern (top, WIP score −1.61, Lg10 p-value = 9.54e-05) versus a strong change in overall initiation levels with minimal change in initiation shape(WIP score −0.13, Log10 p-value = 0.84). (G) Scatter plot of TF motif enrichment in TSRs with significant changes in overall activity versus changes in TSS positions, highlighting differential associations of NF-κB, TEAD, and NFI motifs with these TSRs classes. (H) Venn diagram showing the overlap of ChIP-seq peaks for NFIA and TEAD4 before and after IL-1B stimulation in astrocytes. (I) Motif enrichment analysis of condition-specific (either Veh or IL-1B) TEAD4- and NFIA-bound regions, showing IL-1B-specific enrichment for inflammatory TF motifs, including NF-κB, IRF (IRF8), and AP1 (i.e. Fra1).

Article Snippet: Two days before collection, the astrocytes were plated at a density of 500,000 cells per well on 4-well chamber slides to perform immunocytochemistry or a density of 5.5 million cells per 15 cm dish to be treated with 10ng/mL of recombinant human interleukin 1 beta (IL-1B) (Invivogen, Cat#rcyec-h) for 1hr before sample collection.

Techniques: RNA Sequencing, Gene Expression, ChIP-sequencing, Activity Assay

Journal: bioRxiv

Article Title: Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

doi: 10.64898/2026.05.03.722406

Figure Lengend Snippet: (A) Venn diagram showing overlap between IL-1B-induced genes in astrocytes and KLA-induced genes in bone marrow-derived macrophages (BMDMs). (B) Venn diagram showing overlap between induced TSRs in astrocytes and BMDMs, revealing largely distinct stimulus-responsive enhancer landscapes despite partial overlap in induced genes. (C) Genome browser view of Tnfaip3 locus illustrating that astrocytes and BMDMs induce the same gene but use different enhancers upstream a shared promoter. (D) Top: Venn diagram showing overlap of NF-κB binding sites between activated astrocytes and BMDMs. Bottom: Fraction of astrocyte-specific, shared, and BMDM-specific p65 peaks associated with TSRs induced in astrocytes only, in both cell types, and in BMDM only. (E) Heatmap of de novo motif enrichment at cell type-specific induced TSRs, showing enrichment of lineage-associated motifs for each cell type. (F) Fraction of induced TSR classes bound by lineage-associated TFs, showing preferential association of astrocyte-induced TSRs with NFI and TEAD4 and macrophage-induced TSRs with PU.1 and CEBPα.

Article Snippet: Two days before collection, the astrocytes were plated at a density of 500,000 cells per well on 4-well chamber slides to perform immunocytochemistry or a density of 5.5 million cells per 15 cm dish to be treated with 10ng/mL of recombinant human interleukin 1 beta (IL-1B) (Invivogen, Cat#rcyec-h) for 1hr before sample collection.

Techniques: Derivative Assay, Binding Assay

Journal: bioRxiv

Article Title: Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

doi: 10.64898/2026.05.03.722406

Figure Lengend Snippet: (A) Average eRNA signal centered on astrocyte-specific, shared, and BMDM-specific NF-κBp65 peaks, showing cell type-matched induction of regulatory transcription at p65 bound sites. (B) Fraction of astrocyte-specific, shared, and BMDM-specific p65 peaks overlapping accessible chromatin regions in astrocytes or BMDMs, indicating that NF-κB recruitment occurs preferentially at cell-type-specific open chromatin regions. (C) Violin plots showing increase in ChIP-seq signal for p65, NFIA, TEAD4 at astrocyte IL-1B-induced TSRs and for p65, PU.1, and CEBPβ in macrophage KLA-induced TSRs.

Article Snippet: Two days before collection, the astrocytes were plated at a density of 500,000 cells per well on 4-well chamber slides to perform immunocytochemistry or a density of 5.5 million cells per 15 cm dish to be treated with 10ng/mL of recombinant human interleukin 1 beta (IL-1B) (Invivogen, Cat#rcyec-h) for 1hr before sample collection.

Techniques: ChIP-sequencing

Journal: bioRxiv

Article Title: Microbiome-derived hydroxyphenyl propanoates enhance antitumour immunity by potentiating gasdermin D activity in tumour-associated myeloid cells

doi: 10.64898/2026.04.23.720410

Figure Lengend Snippet: a, IL-1β activity in the supernatant of THP1-WT vs. - GSDMD -KO cells treated with LPS±HPPs for 16 hours, measured using HEK-Blue™ IL-1β reporter cells (three combined experiments, error bars represent standard error, one-way ANOVA with Bonferroni test); b, LDH release from THP1-WT vs. – GSDMD -KO cells treated with LPS±HPP for 16 hours (three combined experiments, one-way ANOVA with Bonferroni test); c-d, IL-1β activity in the supernatant of THP1-WT vs. - GSDMD -KO cells © and human PBMCs (d) treated with LPS and NG±HPPs for 16 hours. measured using HEK-Blue™ IL-1β reporter cells (three combined experiments, error bars represent standard error, one-way ANOVA with Bonferroni test); e-f, LDH release from THP1-WT vs. – GSDMD -KO cells € and human PBMCs (f) treated with LPS and NG±HPPs for 16 hours (three combined experiments, one-way ANOVA with Bonferroni test).

Article Snippet: To neutralize IL-1 receptor signalling, the following antibodies were used: anti-human IL-1α (1 μg/mL; clone 7D4; mabg-hil1a-3; InvivoGen), anti-human IL-1β (1 μg/mL; clone 4H5; mabg-hil1b-3; InvivoGen) and IgG1 isotype control (1 μg/mL; clone T8E5; mabg1-ctrlm; InvivoGen).

Techniques: Activity Assay

Journal: bioRxiv

Article Title: Microbiome-derived hydroxyphenyl propanoates enhance antitumour immunity by potentiating gasdermin D activity in tumour-associated myeloid cells

doi: 10.64898/2026.04.23.720410

Figure Lengend Snippet: a-b, tumour growth kinetics and OS for orthotopic M3-9-M OVA tumours in male WT or Gsdmd -KO mice receiving vehicle or 3,2-HPP treatments from day 1 post cell-implantation (n =8/group; two combined experiments, two-way ANOVA test for growth kinetics, Log-Rank test for OS); c, [IL-1β] in interstitial fluid harvested from 18-day old M3-9-M OVA tumours grown in male WT or Gsdmd -KO mice receiving vehicle or 3,2-HPP treatment from day 1 post-cell implantation (two combined experiments, one-way ANOVA with Bonferroni multiple comparison test); d, GSDMD peptides quantified from a publicly available tumour proteomic database established from stage IV melanoma patients undergoing anti-PD-1 treatment (responder, R = 40 and non-responder, NR = 27); e-g, correlation uncleaved GSDMD peptide with NFKB1 gene targets and two sets of M1- vs. M2-like macrophage gene signatures, respectively, in stage IV melanoma patients undergoing anti-PD-1 treatment (R = 18 and NR = 6, chi-square test).

Article Snippet: To neutralize IL-1 receptor signalling, the following antibodies were used: anti-human IL-1α (1 μg/mL; clone 7D4; mabg-hil1a-3; InvivoGen), anti-human IL-1β (1 μg/mL; clone 4H5; mabg-hil1b-3; InvivoGen) and IgG1 isotype control (1 μg/mL; clone T8E5; mabg1-ctrlm; InvivoGen).

Techniques: Comparison