Journal: bioRxiv

Article Title: Histone H4 acetyl-methyllysine marks accessible chromatin that resists compaction

doi: 10.64898/2026.04.17.718779

Figure Lengend Snippet: ( A ) Relative promoter accessibility (±50 bp of the TSS) in HEK293T cells as determined by ATAC-seq. Normalized ATAC-seq signal was binned by promoter Kacme levels (±1 kb of the TSS) as determined by ChIP-seq. ( B ) Genome browser visualization of ATAC-seq and Kacme ChIP-seq profiles at selected loci on chromosome 19 in HEK293T cells. ( C ) Heatmaps of Kacme ChIP-seq and H3K27me3 CUT&RUN signal centered on transcription start sites (±2.5 kb) across all annotated HEK293T promoter regions. ( D ) Relative promoter accessibility in HEK293T cells for genes in the 25 th or 75 th percentiles of Kacme CUT&RUN levels. Data are binned by H4K5ac CUT&RUN signal. ( E ) Left: Representative western blot of histones from HEK293T cells treated with the transcription inhibitors triptolide (10 μM, 1 h) or flavopiridol (500 nM, 1 h). Right: Venn diagram showing the overlap between genes with a promoter-proximal Kacme peak (±3 kb of the TSS) in untreated HEK293T cells (light blue) and in triptolide-treated HEK293T cells (light red). Kacme peaks were identified using MACS2. ( F ) Genome browser tracks showing ATAC-seq, Kacme, H3K4me1, H3K27ac, and H3K4me3 signal profiles across an enhancer-rich locus in HEK293T cells. ( G ) Heatmaps and aggregated signal profiles for ATAC-seq, Kacme, H3K27ac, H3K4me1, and H3K27me3 across six enhancer clusters identified in HEK293T cells by k-means clustering. Aggregated profiles show the mean signal across enhancer regions within each cluster. ( H ) HOMER known motif analysis for enhancer clusters 1 and 2 , showing the top 20 enriched motifs with their best-match transcription factors and associated p-values. FOX proteins highlighted in magenta, CTCF highlighted in green. ( A, D ) Distribution means compared with two-tailed unpaired Wilcoxon test for two biological replicates. *** = p < 0.001.

Article Snippet: For transcriptional inhibition studies, HEK293T cells were treated with 10 μM triptolide (MCE, HY-32735) or 500 nM flavopiridol (Sigma Aldrich, F3055) for 1hr.

Techniques: ChIP-sequencing, Western Blot, Two Tailed Test

Journal: bioRxiv

Article Title: Histone H4 acetyl-methyllysine marks accessible chromatin that resists compaction

doi: 10.64898/2026.04.17.718779

Figure Lengend Snippet: ( A ) Relative promoter accessibility in THP-1 cells for genes in the 25 th or 75 th percentiles of Kacme ChIP-seq levels. Data are binned by H4K5ac ChIP-seq signal. ( B ) Relative promoter accessibility in THP-1 cells for genes in the 25 th or 75 th percentiles of Kacme ChIP-seq levels. Data are binned by H3K27ac ChIP-seq signal. ( C ) Genome browser visualization of Kacme ChIP-seq (untreated) and Kacme CUT&RUN (triptolide-treated) profiles at representative loci on chromosome 5 in HEK293T cells. ( B-C ) Distribution means compared with two-tailed unpaired Wilcoxon test for two biological replicates. *** = p < 0.001; * = p < 0.05; NS = Not Significant.

Article Snippet: For transcriptional inhibition studies, HEK293T cells were treated with 10 μM triptolide (MCE, HY-32735) or 500 nM flavopiridol (Sigma Aldrich, F3055) for 1hr.

Techniques: ChIP-sequencing, Two Tailed Test

Journal: Frontiers in Pharmacology

Article Title: Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis

doi: 10.3389/fphar.2026.1834558

Figure Lengend Snippet: Triptolide promotes the clearance of intracellular SA and MRSA. (A) Schematic diagram of the procedure for screening TCM monomers that modulate intracellular SA clearance. (B) Representative results illustrating the effects of 15 TCM monomers that promoted intracellular SA clearance and 2 that inhibited it. DMSO and methicillin were used as the negative and positive controls, respectively. Intracellular survival analysis of SA (C) and MRSA (D) in iBMDMs treated with different concentrations of the designated TCM monomers. Data are shown as mean ± SEM [n = 3 in (B–D) ]. ***0.0001 ≤ P < 0.001; **** P < 0.0001 [one-way ANOVA with Dunnett’s post hoc test for (B–D) ].

Article Snippet: For transcriptomics analysis, total RNA was extracted from iBMDMs infected with SA and treated with DMSO or triptolide, and from lung macrophages of mice infected with SA or MRSA treated with PBS, triptolide, or methicillin according to the TRIzol® manual (Life Technologies, 15596-026).

Techniques:

Journal: Frontiers in Pharmacology

Article Title: Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis

doi: 10.3389/fphar.2026.1834558

Figure Lengend Snippet: Triptolide triggers activation of the apoptotic signaling pathway. Gene Ontology (GO) enrichment analysis of differentially expressed genes (A) and proteins (B) in SA-infected iBMDMs treated with triptolide versus DMSO. Volcano maps depicting differentially expressed genes (C) and proteins (D) in SA-infected iBMDMs treated with triptolide versus DMSO. (E) Representative results of fluorescence-activated cell sorting (FACS)-based analysis for percentages of apoptotic cells. Quantification of apoptosis in SA (F) - and MRSA (G) -infected cells treated with DMSO, triptolide, or methicillin. Immunoblotting analysis of cleaved caspase-3 in SA (H) - and MRSA (I) -infected cells treated with DMSO, triptolide, or methicillin. Q-VD-OPh was used as the caspase inhibitor. Data are shown as mean ± SEM [n = 4 in (F,G) ]. **** P < 0.0001 [two-way ANOVA with Tukey’s post-hoc test for (F,G) ].

Article Snippet: For transcriptomics analysis, total RNA was extracted from iBMDMs infected with SA and treated with DMSO or triptolide, and from lung macrophages of mice infected with SA or MRSA treated with PBS, triptolide, or methicillin according to the TRIzol® manual (Life Technologies, 15596-026).

Techniques: Activation Assay, Infection, Fluorescence, FACS, Western Blot

Journal: Frontiers in Pharmacology

Article Title: Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis

doi: 10.3389/fphar.2026.1834558

Figure Lengend Snippet: Triptolide induces apoptosis through targeting XIAP. (A) Measurement of triptolide binding affinity to Bcl2, STAT1, and XIAP by octet. (B) Molecular docking analysis between triptolide and XIAP. The BIR2 and BIR3 domains of XIAP are shown in orange. RMSD (C) and Rg (D) curves depicting the interaction between triptolide and XIAP. RMSD, root mean square deviation; Rg, radius of gyration. (E) Blocking assay to assess the effect of triptolide or SM-164 on XIAP-caspase-3/9 interaction. Quantification of apoptosis in SA (F) - and MRSA (G) -infected cells treated with DMSO, triptolide, SM-164, triptolide in combination with SM-164, or methicillin. Data are shown as mean ± SEM [n = 3 in (F,G) ]. **0.001 ≤ P < 0.01; ***0.0001 ≤ P < 0.001; **** P < 0.0001 [one-way ANOVA with Dunnett’s post hoc test for (F,G) ].

Article Snippet: For transcriptomics analysis, total RNA was extracted from iBMDMs infected with SA and treated with DMSO or triptolide, and from lung macrophages of mice infected with SA or MRSA treated with PBS, triptolide, or methicillin according to the TRIzol® manual (Life Technologies, 15596-026).

Techniques: Binding Assay, Blocking Assay, Infection

Journal: Frontiers in Pharmacology

Article Title: Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis

doi: 10.3389/fphar.2026.1834558

Figure Lengend Snippet: Triptolide reduces SA and MRSA survival and attenuates host inflammatory pathology in vivo (A) Diagram of the experimental design in mice. Bacterial loads of SA (B) and MRSA (C) in the lungs of C57BL/6N mice treated with PBS, triptolide, or methicillin. (D) Representative images and quantitation for inflammatory areas in the lungs of C57BL/6N mice treated as in (B,C) . Scale bar, 100 μm. (E) Immunofluorescence and quantitation for cleaved caspase-3 (red) in the lung macrophages (green) of C57BL/6N mice treated as in (B,C) . Scale bar, 20 μm. Data are shown as mean ± SEM [n = 4 in (B–E) ]. *0.01 ≤ P < 0.5; **0.001 ≤ P < 0.01; ***0.0001 ≤ P < 0.001; **** P < 0.0001 [one-way ANOVA with Tukey’s post-hoc test for (B–E) ].

Article Snippet: For transcriptomics analysis, total RNA was extracted from iBMDMs infected with SA and treated with DMSO or triptolide, and from lung macrophages of mice infected with SA or MRSA treated with PBS, triptolide, or methicillin according to the TRIzol® manual (Life Technologies, 15596-026).

Techniques: In Vivo, Quantitation Assay, Immunofluorescence

Journal: Frontiers in Pharmacology

Article Title: Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis

doi: 10.3389/fphar.2026.1834558

Figure Lengend Snippet: Transcriptomics and proteomics analysis revealing that triptolide induces apoptosis in lung macrophages from mice infected with SA or MRSA. (A) GO enrichment analysis of differentially expressed genes in SA-infected mice treated with PBS, triptolide, or methicillin. (B) GO enrichment analysis of differentially expressed genes in MRSA-infected mice treated with PBS, triptolide, or methicillin. (C) GO enrichment analysis of differentially expressed proteins in mice treated as in (A) . (D) GO enrichment analysis of differentially expressed proteins in mice treated as in (B) .

Article Snippet: For transcriptomics analysis, total RNA was extracted from iBMDMs infected with SA and treated with DMSO or triptolide, and from lung macrophages of mice infected with SA or MRSA treated with PBS, triptolide, or methicillin according to the TRIzol® manual (Life Technologies, 15596-026).

Techniques: Transcriptomics, Infection

Journal: Frontiers in Pharmacology

Article Title: Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis

doi: 10.3389/fphar.2026.1834558

Figure Lengend Snippet: Metagenomics analysis revealing that triptolide maintains microbiota homeostasis in mice infected with SA or MRSA. (A) Alpha (α) diversity among SA-infected mice treated with PBS, triptolide, or methicillin. (B) Alpha (α) diversity among MRSA-infected mice treated with PBS, triptolide, or methicillin. (C) Differential analysis of gut microbial composition among SA-infected mice treated as in (A) . (D) Differential analysis of gut microbial composition among MRSA-infected mice treated as in (B) .

Article Snippet: For transcriptomics analysis, total RNA was extracted from iBMDMs infected with SA and treated with DMSO or triptolide, and from lung macrophages of mice infected with SA or MRSA treated with PBS, triptolide, or methicillin according to the TRIzol® manual (Life Technologies, 15596-026).

Techniques: Metagenomics, Infection

Journal: Frontiers in Pharmacology

Article Title: Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis

doi: 10.3389/fphar.2026.1834558

Figure Lengend Snippet: Metabolomics analysis revealing that triptolide enhances immunomodulatory metabolites against infections. (A) Partial least-squares discriminant analysis (PLS-DA) score plots of metabolites from SA-infected mice treated with PBS, triptolide, or methicillin. (B) PLS-DA score plots of metabolites from MRSA-infected mice treated with PBS, triptolide, or methicillin. (C) Heatmap of differential metabolites among SA-infected mice treated as in (A) . (D) Heatmap of differential metabolites among MRSA-infected mice treated as in (B) .

Article Snippet: For transcriptomics analysis, total RNA was extracted from iBMDMs infected with SA and treated with DMSO or triptolide, and from lung macrophages of mice infected with SA or MRSA treated with PBS, triptolide, or methicillin according to the TRIzol® manual (Life Technologies, 15596-026).

Techniques: Infection