Journal: The FASEB Journal

Article Title: Endothelial Matrin‐3 Limits Cellular Senescence and Lipid Dysregulation to Protect Against Murine Atherosclerosis

doi: 10.1096/fj.202602809RR

Figure Lengend Snippet: Matrin‐3 silencing alters the proteome in Human Umbilical Vein Endothelial Cells. (A) Schematic depicting the workflow of quantitative proteomics by TMT10 plex labeling followed by mass spectrometry and analysis. (B) Principal component analysis. (C) A volcano plot showing the differentially expressed proteins by quantitative proteomics in HUVECs. (D) Top Hallmark terms and KEGG pathways identified by Enrichr analysis. Gene symbols of the identified proteins were used for analysis. (E) Matrin‐3, p53, p21, and p16 protein expression by Western blot analysis.

Article Snippet: The following primary antibodies were used: anti‐Matrin‐3 (Bethyl Laboratories #A300‐591A; 1:1000 dilution), p53 (Santa Cruz Biotechnology, cat# sc‐126×; 1:5000 dilution), p21 (Cell Signaling Technology, cat# 2947S; 1:1000 dilution), p16 (Abcam, cat# ab108349; 1:1000 dilution), and anti‐GAPDH (Cell Signaling Technology, cat# 2118S; 1:10000 dilution).

Techniques: Quantitative Proteomics, Labeling, Mass Spectrometry, Analysis, Expressing, Western Blot, shRNA, Significance Assay

Journal: The FASEB Journal

Article Title: Endothelial Matrin‐3 Limits Cellular Senescence and Lipid Dysregulation to Protect Against Murine Atherosclerosis

doi: 10.1096/fj.202602809RR

Figure Lengend Snippet: Matrin‐3 silencing alters the transcriptome in Human Coronary Artery Endothelial Cells. (A) Schematic depicting the workflow. (B) Principal component analysis showing the data variation among samples and a MA plot showing the differentially expressed genes identified by bulk RNA‐seq. (C) Top Hallmark terms and KEGG pathways identified by Enrichr analysis. 3136 differential genes ( p adj < 0.05) were used for analysis. (D) Gene symbols of differential proteins were overlapped with the differentially expressed genes identified by bulk RNA‐seq. Common differential genes were used for Enrichr analysis to identify enriched Hallmark terms and KEGG pathways.

Article Snippet: The following primary antibodies were used: anti‐Matrin‐3 (Bethyl Laboratories #A300‐591A; 1:1000 dilution), p53 (Santa Cruz Biotechnology, cat# sc‐126×; 1:5000 dilution), p21 (Cell Signaling Technology, cat# 2947S; 1:1000 dilution), p16 (Abcam, cat# ab108349; 1:1000 dilution), and anti‐GAPDH (Cell Signaling Technology, cat# 2118S; 1:10000 dilution).

Techniques: Analysis, RNA Sequencing, shRNA, Significance Assay

Journal: Bone Research

Article Title: Integrated stress signaling pathways promote adaptive reprogramming for chondrocyte survival in Metaphyseal Chondrodysplasia Type Schmid

doi: 10.1038/s41413-026-00587-5

Figure Lengend Snippet: Dynamic changes in p53/p63 and regulators, ASPP2 and iASPP in 13del-MCDS mice hypertrophic chondrocytes. a Immunohistochemistry staining of p53 on the 10-day-old proximal tibia growth plate. Specific regions of the hypertrophic zone (HZ) in +/+ and M/M mice are shown in higher magnification, illustrating very low staining in +/+ in regions 1, 2, and 3. Whereas in M/M mice, there are varying low (L1, L2, and L3) and high (H1, H2, and H3) p53-expressing regions. b Co-immunofluorescence staining of p53 and DAPI showing p53 in +/+ HCs is cytoplasmic, whereas in M/M mice, p53 is primarily localized to the nucleus (yellow arrowheads). c Immunohistochemistry staining of Tap63 showed an upregulation in M/M HCs (black arrowheads). d Immunohistochemistry staining of ΔNp63 showed a downregulation in M/M HCs. e Immunofluorescence staining of ASPP2 and f iASPP proteins on 10-day-old proximal tibia growth plates, showing a differential and dynamic down- and up-regulation in HCs of M/M mice, respectively. Scale bar = 50 μm

Article Snippet: It was subsequently probed with an appropriately diluted primary antibody overnight at 4 o C. The next step was incubation with a horseradish peroxidase-conjugated secondary antibody (which recognized the primary antibody) for 30 min. Immunohistochemistry and immunofluorescence staining were performed using antibodies specific for Collagen X and 13del mutant Collagen X (Generated by our lab ), Cyclin D1 (Santa Cruz, Cat#sc-753), Xbp1s (BioLegend, Cat# 647502), CD31 (Abcam, Cat# ab28364), HIF1a (SANTA CRUZ BIOTECH, Cat# sc-10790), HIF2a (SANTA CRUZ BIOTECH, Cat# sc-28706), p53 (E-19) (SANTA CRUZ BIOTECH, Cat# sc-1315), Tap63 (NOVUS BIOLOGICALS, Cat# NBP3-11703), ΔNp63 (BioLegend, Cat# 619001), EDEM (Provided by Kumamoto University, Japan), iASPP (Sigma, Cat# A4605), ASPP2 (Provided by Dr. Xin Lu from University of Oxford), ATF4 (SANTA CRUZ BIOTECH, Cat# sc-200), p57Kip2 (SANTA CRUZ BIOTECH, Cat# sc-56341), EF5-Cy3 regular stain antibody and EF5-competed stain antibody (Provided by Dr. Cameron Koch from University of Pennsylvania Department of Radiation Oncology), Map-LC3B (MBL life science, Cat# PM036), CHOP (SANTA CRUZ BIOTECH, Cat# sc-166682), GADD34 (SANTA CRUZ BIOTECH, Cat# sc-794), ATF3 (SANTA CRUZ BIOTECH, Cat# sc-81189), 488 Goat Anti-Rabbit IgG (Life technologies, Cat# A-11008) were used.

Techniques: Immunohistochemistry, Staining, Expressing, Immunofluorescence

Journal: Bone Research

Article Title: Integrated stress signaling pathways promote adaptive reprogramming for chondrocyte survival in Metaphyseal Chondrodysplasia Type Schmid

doi: 10.1038/s41413-026-00587-5

Figure Lengend Snippet: Protein clearance is correlated with the hypertrophic chondrocyte differentiation status. a Immunohistochemistry staining of Collagen type X on paraffin sections of the tibia proximal growth plate from 4-week-old M/M mice. Scale bar = 50 μm. b Immunohistochemistry staining of p53 on paraffin sections of the tibia proximal growth plate from 4-week-old M/M mice. Scale bar = 50 μm. c Immunohistochemistry staining of Edem on paraffin sections of the tibia proximal growth plate from P10 M/M mice. d Immunofluorescence staining of Map1-lc3b on paraffin sections of the tibia proximal growth plate from 4-week-old M/M mice and their littermate controls. Boxed regions are the amplified dotted area. e Chloroquine was administered to M/M mice to monitor the dynamics of autophagy activity by blocking the fusion of autophagosomes with lysosomes. Immunofluorescence staining and quantification of LC3 puncta cells demonstrated an increase in LC3 puncta-positive cells in the UHZ and LHZ of MCDS mice after the chloroquine administration. UHZ (1, 1’): the upper hypertrophic zone; MHZ (2, 2’): the middle hypertrophic zone; LHZ (3, 3’): the lower hypertrophic zone

Article Snippet: It was subsequently probed with an appropriately diluted primary antibody overnight at 4 o C. The next step was incubation with a horseradish peroxidase-conjugated secondary antibody (which recognized the primary antibody) for 30 min. Immunohistochemistry and immunofluorescence staining were performed using antibodies specific for Collagen X and 13del mutant Collagen X (Generated by our lab ), Cyclin D1 (Santa Cruz, Cat#sc-753), Xbp1s (BioLegend, Cat# 647502), CD31 (Abcam, Cat# ab28364), HIF1a (SANTA CRUZ BIOTECH, Cat# sc-10790), HIF2a (SANTA CRUZ BIOTECH, Cat# sc-28706), p53 (E-19) (SANTA CRUZ BIOTECH, Cat# sc-1315), Tap63 (NOVUS BIOLOGICALS, Cat# NBP3-11703), ΔNp63 (BioLegend, Cat# 619001), EDEM (Provided by Kumamoto University, Japan), iASPP (Sigma, Cat# A4605), ASPP2 (Provided by Dr. Xin Lu from University of Oxford), ATF4 (SANTA CRUZ BIOTECH, Cat# sc-200), p57Kip2 (SANTA CRUZ BIOTECH, Cat# sc-56341), EF5-Cy3 regular stain antibody and EF5-competed stain antibody (Provided by Dr. Cameron Koch from University of Pennsylvania Department of Radiation Oncology), Map-LC3B (MBL life science, Cat# PM036), CHOP (SANTA CRUZ BIOTECH, Cat# sc-166682), GADD34 (SANTA CRUZ BIOTECH, Cat# sc-794), ATF3 (SANTA CRUZ BIOTECH, Cat# sc-81189), 488 Goat Anti-Rabbit IgG (Life technologies, Cat# A-11008) were used.

Techniques: Immunohistochemistry, Staining, Immunofluorescence, Amplification, Activity Assay, Blocking Assay

Journal: Bone Research

Article Title: Integrated stress signaling pathways promote adaptive reprogramming for chondrocyte survival in Metaphyseal Chondrodysplasia Type Schmid

doi: 10.1038/s41413-026-00587-5

Figure Lengend Snippet: Proposed mechanism linking ER stress to integrated survival signaling in 13del-MCDS hypertrophic chondrocytes. A 13-bp deletion in Col10a1 leads to production of misfolded collagen X and its accumulation within the endoplasmic reticulum (ER) of HCs, triggering ER stress. ER stress activates ATF4 and hypoxia/HIF signaling as an intrinsic adaptive response. In parallel, p53 signaling and autophagy are engaged. Autophagy facilitates the clearance of accumulated misfolded proteins, thereby reducing proteotoxic stress. Collectively, HIF, ATF4, p53, and autophagy form an integrated survival network that promotes HC survival, supports metabolic adaptation, and enables cell-cycle re-entry. This coordinated response enables partial adaptation to ER stress and contributes to the growth plate phenotype observed in 13del-MCDS mice

Article Snippet: It was subsequently probed with an appropriately diluted primary antibody overnight at 4 o C. The next step was incubation with a horseradish peroxidase-conjugated secondary antibody (which recognized the primary antibody) for 30 min. Immunohistochemistry and immunofluorescence staining were performed using antibodies specific for Collagen X and 13del mutant Collagen X (Generated by our lab ), Cyclin D1 (Santa Cruz, Cat#sc-753), Xbp1s (BioLegend, Cat# 647502), CD31 (Abcam, Cat# ab28364), HIF1a (SANTA CRUZ BIOTECH, Cat# sc-10790), HIF2a (SANTA CRUZ BIOTECH, Cat# sc-28706), p53 (E-19) (SANTA CRUZ BIOTECH, Cat# sc-1315), Tap63 (NOVUS BIOLOGICALS, Cat# NBP3-11703), ΔNp63 (BioLegend, Cat# 619001), EDEM (Provided by Kumamoto University, Japan), iASPP (Sigma, Cat# A4605), ASPP2 (Provided by Dr. Xin Lu from University of Oxford), ATF4 (SANTA CRUZ BIOTECH, Cat# sc-200), p57Kip2 (SANTA CRUZ BIOTECH, Cat# sc-56341), EF5-Cy3 regular stain antibody and EF5-competed stain antibody (Provided by Dr. Cameron Koch from University of Pennsylvania Department of Radiation Oncology), Map-LC3B (MBL life science, Cat# PM036), CHOP (SANTA CRUZ BIOTECH, Cat# sc-166682), GADD34 (SANTA CRUZ BIOTECH, Cat# sc-794), ATF3 (SANTA CRUZ BIOTECH, Cat# sc-81189), 488 Goat Anti-Rabbit IgG (Life technologies, Cat# A-11008) were used.

Techniques: