Journal: Nature Communications

Article Title: MAT2A promotes atherosclerotic plaque vulnerability by mediating epigenetic reprogramming of macrophages

doi: 10.1038/s41467-025-66121-z

Figure Lengend Snippet: A The enrollment of TCFA-positive patients defined by OCT and schematic representation of the patients screened in the discovery cohort. This figure was created using images from PowerPoint and BioRender. Created in BioRender. wan, p. (2025) https://BioRender.com/dmkgnf0 . B Partial least-squares discrimination analysis (PLS-DA) 3D score plots. C Volcano plot of significantly differential metabolites in monocytes. D Detection of monocytes methionine metabolism concentrations ( n = 38 subjects). E The final FCT was determined by averaging three measurements performed at the thinnest part of the fibrous cap. F Vulnerable plaque characteristics between patients with high and low SAM/SAH levels ( n = 38 subjects). G Multivariate logistic regression analysis revealing the relationship between high SAM/SAH levels and TCFA ( n = 76 for total subjects). H Representative OCT images of a normal coronary artery, a vulnerable plaque, and a stable plaque. Scale bar = 5 mm. I Schematic of the methionine metabolism pathway. J The mRNA levels in monocytes isolated from TCFA-positive and TCFA-negative individuals ( n = 38 subjects). UMAP visualization ( K ) and MAT2A expression ( L ) of human atherosclerotic carotid artery cells ( n = 15 patients, GSE253903 ). UMAP visualization ( M ) and MAT2A expression ( N ) of human atherosclerotic carotid artery myeloid cells. Representative immunofluorescence images ( O ) and quantification ( P ) of MAT2A and CD11b in carotid plaques from symptomatic and asymptomatic patients ( n = 6 subjects. Scale bar = 50 µm). C Two-tailed P-values were indicated. D The bar bands defined as 25th and 75th percentiles; the plot top line as median; two-tailed Mann–Whitney P -values are indicated. F The box shows the 25th, 50th and 75th percentiles of the data. The whiskers represent minimum and the maximum; Chi-squared test and two-tailed Mann–Whitney P -values was used. G The error bars represent the 95% CI for the OR, with their centers (red squares) indicating the point estimates; two-tailed P -values are shown. ( J , P ) Data are presented as the mean ± SD; two-tailed P -values are shown. L , N Log normalized using the ‘NormalizeData’ function in Seurat with default parameters. CKD chronic kidney disease, FCT fibrous cap thickness, MAT2A methionine adenosyltransferase Ⅱ alpha, OCT optical coherence tomography, SAH, S-adenosyl-homocysteine, SAM S-adenosyl-methionine, TCFA thin-cap fibroatheroma, UMAP uniform manifold approximation and projection. Source data are provided as a Source Data file.

Article Snippet: Sections were then incubated overnight at 4 °C with primary antibodies against MAT2A (1:200, sc-398917, Santa Cruz Biotechnology, USA), CD11b (1:200, ab128797, Abcam, UK), CD68 (1:100, ab125212, Abcam, UK), and H3K4me3 (1:500, 39060, Active Motif, Shanghai, China).

Techniques: Isolation, Expressing, Immunofluorescence, Two Tailed Test, MANN-WHITNEY, Tomography

Journal: Nature Communications

Article Title: MAT2A promotes atherosclerotic plaque vulnerability by mediating epigenetic reprogramming of macrophages

doi: 10.1038/s41467-025-66121-z

Figure Lengend Snippet: Both groups of 8-week-old female and male MAT2A fl/fl ApoE -/- and MAT2A CKO ApoE -/- mice were fed an HFD for 16 weeks. A Schematic figure showing the experimental strategy for the HFD feeding and the subsequent analysis. This figure was created using images from Photoshop and BioRender. Created in BioRender. wan, p. (2025) https://BioRender.com/3iunh0m . B SAM and SAH concentrations as well as SAM/SAH ratio for mice monocyte cell lysate mass spectrometry samples ( n = 6). C Representative photographs of atherosclerotic plaques in the aortic arches and their branches in the 2 groups ( n = 10 mice per genotype). Representative images and quantification of Oil Red O-stained aortas ( D , n = 10 samples. Scale bar = 2 mm) and aortic roots ( E , n = 10 independent experiments. Scale bar = 200 µm). F , H , E and Masson’s trichrome staining of representative aortic root sections. Scale bar = 200 µm. G Quantification of plaque area, necrotic core, and collagen ( n = 10 samples). H and I , Immunohistochemistry of CD68 + macrophages and vulnerability index in the aortic roots ( n = 10 samples). Scale bar = 100 µm. Data are presented as the mean ± SD and comparisons were made using unpaired Student’s t -test; the two-tailed P -values are shown. α-SMA α-smooth muscle actin, HFD high-fat diet. Source data are provided as a Source Data file.

Article Snippet: Sections were then incubated overnight at 4 °C with primary antibodies against MAT2A (1:200, sc-398917, Santa Cruz Biotechnology, USA), CD11b (1:200, ab128797, Abcam, UK), CD68 (1:100, ab125212, Abcam, UK), and H3K4me3 (1:500, 39060, Active Motif, Shanghai, China).

Techniques: Mass Spectrometry, Staining, Immunohistochemistry, Two Tailed Test

Journal: Nature Communications

Article Title: MAT2A promotes atherosclerotic plaque vulnerability by mediating epigenetic reprogramming of macrophages

doi: 10.1038/s41467-025-66121-z

Figure Lengend Snippet: A Bubble chart of GO term enrichment analysis of downregulated DEGs based on RNA-seq in BMDMs of MAT2A CKO compared with MAT2A fl/fl mice. Flow cytometry was performed to quantify CD45 + CD11b + CD115 + Ly6C hi monocytes from bone marrow or peripheral blood ( B , n = 6 independent experiments), MHC Ⅱ and CCR2 ( C , n = 6 samples) on CD45 + CD68 + macrophages from aortic plaques of MAT2A CKO ApoE -/- and MAT2A fl/fl ApoE -/- mice fed a 16-week HFD. D – J Analysis of BMDMs from MAT2A CKO and MAT2A fl/fl mice treated with or without SAM (200 µM) following LPS and IFN-γ stimulation. Representative flow cytometry plots and quantification of CD45 + CD11b + CD86 + macrophages ( D , n = 6 samples), transwell ( E , n = 6 samples, Scale bar = 100 µm), and wound assay ( F , n = 6 samples. Scale bar = 500 µm). The mRNA levels of Il1b , Il6 , Nos2 ( G , n = 6 samples) and Ccl2 , Ccl7 and Cxcl1 ( H , n = 6 samples) measured by qRT-PCR. I , J The THP-1 cells were transfected with siNC or siMAT2A followed by LPS and IFN-γ treatment with or without SAM (200 µM). The mRNA levels of Il1b , Il6 , Nos2, Ccl2 , Ccl7 and Cxcl1 were analyzed by qRT-PCR ( n = 6 samples). A P -values were derived from hypergeometric distribution. Data are presented as the mean ± SD. B , C Unpaired Student’s t -test was used; two-tailed P values are shown. D – J One-way ANOVA was used; the adjusted P -values are shown. 8-week-old female and male mice were both used. BL blood, BM bone marrow, BMDMs bone marrow-derived macrophages, DEGs differentially expressed genes, GO gene ontology, IFN-γ interferon-γ, LPS lipopolysaccharide. Source data are provided as a Source Data file.

Article Snippet: Sections were then incubated overnight at 4 °C with primary antibodies against MAT2A (1:200, sc-398917, Santa Cruz Biotechnology, USA), CD11b (1:200, ab128797, Abcam, UK), CD68 (1:100, ab125212, Abcam, UK), and H3K4me3 (1:500, 39060, Active Motif, Shanghai, China).

Techniques: RNA Sequencing, Flow Cytometry, Quantitative RT-PCR, Transfection, Derivative Assay, Two Tailed Test

Journal: Nature Communications

Article Title: MAT2A promotes atherosclerotic plaque vulnerability by mediating epigenetic reprogramming of macrophages

doi: 10.1038/s41467-025-66121-z

Figure Lengend Snippet: A Immunoblots of H3K4me3, H3K36me3, and H3K27me3 levels in BMDMs from MAT2A fl/fl and MAT2A CKO mice ( n = 3). B Representative immunofluorescence images and quantification for H3K4me3 and CD68 in aortic root plaque from MAT2A fl/fl ApoE -/- and MAT2A CKO ApoE -/- mice fed a 16-week HFD ( n = 7). Scale bar = 100 µm. C – G Analysis of BMDMs between MAT2A CKO and MAT2A fl/fl mice. C Heatmaps for H3K4me3 binding peaks in BMDMs from MAT2A fl/fl and MAT2A CKO mice. D Venn diagram reflecting overlapping downregulated genes with H3K4me3 modification combining the CUT&Tag and RNA-seq data. Bubble charts of GO ( E ) and KEGG ( F ) analysis according to downregulated genes with decreased H3K4me3 modification. G IGV tracks revealing the results of CUT&Tag reads (H3K4me3 binding) distributions in indicated genes. H , I Analysis of BMDMs between MAT2A CKO and MAT2A fl/fl mice treated with or without SAM (200 µM) in the presence of LPS and IFN-γ. H ChIP-qPCR validation of H3K4me3 enrichment on the promoter regions of Aim2 , Ccl2 , and Mmp9 ( n = 6 samples). I ELISA analysis of AIM2, CCL2, and MMP9 in cellular supernatant ( n = 6 independent experiments). Data are presented as the mean ± SD. A , B Unpaired Student’s t -test was used; two-tailed P values are shown. E P -values were derived from hypergeometric distribution. H and I One-way ANOVA was used; the adjusted P -values are shown. Both 8-week-old female and male mice were used. ChIP-qPCR chromatin immunoprecipitation-qPCR, H3K4me3 histone h3 lysine 4 trimethylation, H3K27me3 histone H3 lysine 27 trimethylation, H3K36me3 histone h3 lysine 36 trimethylation, KEGG kyoto encyclopedia of genes and genomes, TSS translation start site. Source data are provided as a Source Data file.

Article Snippet: Sections were then incubated overnight at 4 °C with primary antibodies against MAT2A (1:200, sc-398917, Santa Cruz Biotechnology, USA), CD11b (1:200, ab128797, Abcam, UK), CD68 (1:100, ab125212, Abcam, UK), and H3K4me3 (1:500, 39060, Active Motif, Shanghai, China).

Techniques: Western Blot, Immunofluorescence, Binding Assay, Modification, RNA Sequencing, ChIP-qPCR, Biomarker Discovery, Enzyme-linked Immunosorbent Assay, Two Tailed Test, Derivative Assay, Chromatin Immunoprecipitation

Journal: Nature Communications

Article Title: MAT2A promotes atherosclerotic plaque vulnerability by mediating epigenetic reprogramming of macrophages

doi: 10.1038/s41467-025-66121-z

Figure Lengend Snippet: A – I The HFD-fed ApoE -/- mice were received either FIDAS-5 or vehicle every other day for 6 weeks. A, Flowchart illustrating the experimental procedure. This figure was created using images from Photoshop and BioRender. Created in BioRender. wan, p. (2025) https://BioRender.com/h76jjnw . B Representative photographs of atherosclerotic plaques in the aortic arches and their branches. Representative images and quantification of Oil Red O-stained aortas ( C , n = 8. Scale bar = 2 mm) and aortic roots ( D and E , n = 8. Scale bar = 200 µm). F Representative images of H&E and Masson’s trichrome-stained aortic roots. Scale bar = 200 µm. G Quantification of plaque area, percentage of necrotic core, and collagen of aortic roots ( n = 8 per group). H , I Immunohistochemistry of CD68 + macrophages and vulnerability index in the aortic root plaque of FIDAS-5 treated mice, n = 8 per group. Scale bar = 100 µm. J – R Representative images of female and male mice fed MRD or CD for 6 weeks after a 10-week HFD. J Schematic figure showing the experimental strategy and subsequent analysis. This figure was created using images from Photoshop and BioRender. Created in BioRender. wan, p. (2025) https://BioRender.com/h76jjnw . K Representative images of aortic arches and their branches in the indicated group. Representative images and quantification of Oil Red O-stained aortas ( L , n = 8. Scale bar = 2 mm) and aortic roots ( M and N , n = 8. Scale bar = 200 µm). O Representative images of H&E and Masson’s trichrome-stained aortic root. P Quantification of plaque area, percentage of necrotic core, and collagen, n = 8. Scale bar = 200 µm. Q and R Immunohistochemical staining CD68 + macrophages and vulnerability index, n = 8. Scale bar = 100 µm. Data are presented as mean ± SD and comparisons were made using unpaired Student’s t -test; two-tailed P values are shown. 8-week-old female and male ApoE -/- mice were used. FIDAS-5, a MAT2A inhibitor; MRD, methionine-restricted diet. Source data are provided as a Source Data file.

Article Snippet: Sections were then incubated overnight at 4 °C with primary antibodies against MAT2A (1:200, sc-398917, Santa Cruz Biotechnology, USA), CD11b (1:200, ab128797, Abcam, UK), CD68 (1:100, ab125212, Abcam, UK), and H3K4me3 (1:500, 39060, Active Motif, Shanghai, China).

Techniques: Staining, Immunohistochemistry, Immunohistochemical staining, Two Tailed Test

Journal: Nature Communications

Article Title: MAT2A promotes atherosclerotic plaque vulnerability by mediating epigenetic reprogramming of macrophages

doi: 10.1038/s41467-025-66121-z

Figure Lengend Snippet: A Norepinephrine levels in serum from TCFA-positive and TCFA-negative individuals ( n = 38 independent experiments). B Correlation between serum the ratio of SAM/SAH and norepinephrine levels. C The percentage of patients presenting with TCFA in 3 coronary arteries varied according to their levels of the SAM/SAH ratio and norepinephrine. D MAT2A expression in peripheral blood monocytes from 6-OHDA-treated ApoE -/- mice ( n = 3, one representative experiment out of three was shown). E Representative images and quantification of H&E and Oil Red O staining in aortic root treated with 6-OHDA (250 mg/kg) and AAV-MAT2A, n = 6. Scale bar = 100 µm. F Immunoblots of aortic plaques from ApoE -/- mice treated with 6-OHDA ( n = 3). G , Mat2a mRNA expression in BMDMs pre-treated with 20 nM RAPA followed by 10 mM norepinephrine ( n = 6, one representative experiment out of three was shown). H Transcript levels of c-Myc and Mat2a in BMDMs transfected with the indicated siRNAs ( n = 6). I Occupancy analysis of c-MYC by ChIP-qPCR in BMDMs treated with DMSO vehicle or RAPA (20 nM) ( n = 6). A Two-tailed Mann–Whitney P -values are indicated; Data are shown as median with IQR. B Pearson correlation coefficient test was used; the regression coefficients and two-tailed P -values are shown. C Chi-squared test was used; Data are shown as %. D – F Unpaired Student’s t -test was used; the two-tailed P -values are shown; Data are presented as mean ± SD. G , I Two-way ANOVA was used; The adjusted P -values are shown; Data are presented as mean ± SD. H One-way ANOVA was used; The adjusted P -values are shown. 8-week-old female and male ApoE -/- mice were used. Data are presented as mean ± SD. AAV adeno-associated virus, RAPA rapamycin, 6-OHDA 6-Hydroxydopamine. Source data are provided as a Source Data file.

Article Snippet: Sections were then incubated overnight at 4 °C with primary antibodies against MAT2A (1:200, sc-398917, Santa Cruz Biotechnology, USA), CD11b (1:200, ab128797, Abcam, UK), CD68 (1:100, ab125212, Abcam, UK), and H3K4me3 (1:500, 39060, Active Motif, Shanghai, China).

Techniques: Expressing, Staining, Western Blot, Transfection, ChIP-qPCR, Two Tailed Test, MANN-WHITNEY, Virus

Journal: Nature Communications

Article Title: MAT2A promotes atherosclerotic plaque vulnerability by mediating epigenetic reprogramming of macrophages

doi: 10.1038/s41467-025-66121-z

Figure Lengend Snippet: A Study design in the validation cohort. This figure was created using images from PowerPoint and BioRender. Created in BioRender. wan, p. (2025) https://BioRender.com/qbkjhvs . Detection of monocytes SAM and SAH concentrations ( B ), and SAM/SAH ratio ( C ) of TCFA-positive and TCFA-negative individuals ( n = 100 subjects). D Serum norepinephrine levels from TCFA-positive and TCFA-negative individuals ( n = 100 independent experiments). Qualitative and quantitative OCT analysis of vulnerable plaque characteristics between patients with high and low SAM/SAH levels ( E ) or with high and low norepinephrine levels ( F ) ( n = 100 independent experiments). Pearson correlation analysis of monocytes SAM/SAH ratio ( G ) or serum norepinephrine levels ( H ) with the thinnest FCT and mean lipid arc. I Two-tailed Pearson’s linear regression analysis between the SAM/SAH ratio and norepinephrine levels. J Multivariate logistic regression analysis depicting the relationship between the SAM/SAH ratio, norepinephrine levels, and TCFA ( n = 200 for total subjects). K Receiver operating characteristic curve of SAM/SAH, norepinephrine, and combined both for TCFA. L HR for incident 5-year MACE based on multivariable Cox proportional hazards regression analysis. Adjusted for age, gender, traditional coronary risk factors, and statin at discharge ( n = 200 for total subjects). M A Kaplan-Meier survival curve plots the 5-year MACE-free survival among 4 subgroups. N MAT2A-mediated monocyte methionine metabolism is closely associated with the presence of TCFA in patients. MAT2A, which is induced by the norepinephrine–mTOR–c-MYC axis, is critical for endowing monocytes/macrophages with proinflammatory state and migratory capacity during the development of atherosclerosis through H3K4me3 modification. Myeloid-specific MAT2A ablation, pharmacological blockade with FIDAS-5, or a low-methionine diet attenuate monocyte/macrophage inflammation and migration, thereby reducing atherosclerotic progression and plaque vulnerability. This figure was created using images from PowerPoint and BioRender. Created in BioRender. wan, p. (2025) https://BioRender.com/gylosq5 . B – D Two-tailed Mann–Whitney P -values are indicated. E , F The box shows the 25th, 50th and 75th percentiles of the data. The whiskers represent minimum and the maximum. Data are presented as % or median with IQR, Chi-squared test or Mann-Whitney test was used, and two-tailed P -values were calculated. G – I Pearson correlation coefficient test was used; the regression coefficients and two-tailed P -values are shown. J Data points indicate OR, and 95% confidence intervals are represented by line length; two-tailed P -values are shown. K The 95% confidence interval is shown between brackets. L Data points indicate HR and 95% CI were represented by line length. M P -values were calculated with log rank test. HR hazard ratio. Source data are provided as a Source Data file.

Article Snippet: Sections were then incubated overnight at 4 °C with primary antibodies against MAT2A (1:200, sc-398917, Santa Cruz Biotechnology, USA), CD11b (1:200, ab128797, Abcam, UK), CD68 (1:100, ab125212, Abcam, UK), and H3K4me3 (1:500, 39060, Active Motif, Shanghai, China).

Techniques: Biomarker Discovery, Two Tailed Test, Modification, Migration, MANN-WHITNEY

Journal: Advanced Science

Article Title: Activation of USP30 Disrupts Endothelial Cell Function and Aggravates Acute Lung Injury Through Regulating the S‐Adenosylmethionine Cycle

doi: 10.1002/advs.202512807

Figure Lengend Snippet: Depletion of USP30 increases miR‐30a‐5p expression and decreases SAM and DNA methylation in ECs. A) HLMVECs (n = 5) were treated with siCont or siUSP30 for 3 days, and miRNAs were extracted for miRNA‐seq analysis. Shown is a heat map of miRNA expression. MiR‐30a‐5p is highlighted by the black circle. B) Real‐time PCR analysis of miR‐30a‐5p levels in USP30 siRNA‐transfected HLMVECs. Data shown as mean ± SEM, n = 3. C) Score plot of samples from siCont group and the siUSP30 group using the PLS‐DA model. D) HLMVECs (n = 12) were treated with siCont or siUSP30 for 3 days, and then subjected to metabolic analysis. Clustering result shown as a heatmap. Distance measure using Euclidean, and clustering algorithm using ward's method. E) ELISA analysis of SAM levels in USP30 siRNA‐transfected HLMVECs. Data shown as mean ± SEM, n = 3. F) ELISA analysis of global 5‐methylcytosine (5‐mc) in DNA samples from USP30 siRNA‐transfected HLMVECs. Data shown as mean ± SEM, n = 3. G) Real‐time PCR analysis of miR‐30a‐5p levels in 5‐azacytidine (2 µM, 24 h)‐treated HLMVECs. Data shown as mean ± SEM, n = 3. H) The Scheme shows SAM production by MATs. I) Real‐time PCR analysis of miR‐30a‐5p levels in 5‐azacytidine (0.1 mM, 10 h)‐treated HLMVECs. Data shown as mean ± SEM, n = 6. J) Real‐time PCR analysis of miR‐30a‐5p levels in PF9366 (40 µM, 24 h) or MAT2A‐myc‐transfected HLMVECs. Data shown as mean ± SEM, n = 3. K) Real‐time PCR analysis of miR‐30a‐5p levels in USP30 siRNA‐ or USP30 siRNA+MAT2A‐myc‐transfected HLMVECs. Data shown as mean ± SEM, n = 3.

Article Snippet: MAT2A , Rabbit / IgG , 1:1000 , Proteintech, 55309‐1‐AP.

Techniques: Expressing, DNA Methylation Assay, Real-time Polymerase Chain Reaction, Transfection, Enzyme-linked Immunosorbent Assay

Journal: Advanced Science

Article Title: Activation of USP30 Disrupts Endothelial Cell Function and Aggravates Acute Lung Injury Through Regulating the S‐Adenosylmethionine Cycle

doi: 10.1002/advs.202512807

Figure Lengend Snippet: USP30 deubiquitinates and stabilizes MAT2A. A) Immunoblotting analysis of MAT isoforms in USP30 siRNA‐transfected HLMVECs. Data shown as mean ± SEM, n = 3. Images shown were representative immunoblots from three independent experiments. B) Immunoblotting analysis of MAT2A in isolated lung ECs from wild‐type and EC‐USP30KO mice. Data shown as mean ± SEM. C) Real‐time PCR analysis of USP30 and MAT2A mRNA in USP30 siRNA‐transfected HLMVECs. Data shown as mean ± SEM, n = 6. D) Immunoblotting analysis of MAT2A in CHX (20 µM)‐treated HLMVECs (sicont or siUSP30‐transfected). E) USP30‐V5 and MAT2A‐myc‐overexprssed HEK293/TLR4 cells were subjected to immunoprecipitation with Myc tag antibody, followed by V5 and Myc tag immunoblotting (2 sets). F) Co‐immunofluorescence staining of USP30‐V5 and Myc‐MAT2A in HLMEVCs. Yellow dots in the merged image indicate co‐localization of the two proteins. Scale bar, 10 µm. G) HEK293/TLR4 cells were transfected with USP30 siRNA and MAT2A‐myc plasmid. Denatured cell lysates were subjected to immunoprecipitation with Myc tag antibody, followed by ubiquitin immunoblotting (2 sets). H) Scheme shows that USP30 stabilizes MAT2A and increases SAM production and DNA methylation.

Article Snippet: MAT2A , Rabbit / IgG , 1:1000 , Proteintech, 55309‐1‐AP.

Techniques: Western Blot, Transfection, Isolation, Real-time Polymerase Chain Reaction, Immunoprecipitation, Immunofluorescence, Staining, Plasmid Preparation, Ubiquitin Proteomics, DNA Methylation Assay