Journal: Bioactive Materials

Article Title: Apolipoprotein E knockout attenuates vascular graft fibrosis by reducing profibrotic macrophage formation through low-density lipoprotein receptor related protein 1

doi: 10.1016/j.bioactmat.2026.01.029

Figure Lengend Snippet: Profibrotic macrophages increasing fibroblast proliferation via their secreted IGF-1. (a) Dot plots of Igf1 expression in C2 and the other subgroups of macrophages in regenerated aortas 30 and 90 days after graft implantation in WT and Apoe −/− rats. (b) Igf1 expression score in macrophages in regenerated aortas 30 and 90 days after graft implantation in WT and Apoe −/− rats. ∗∗∗∗ indicates p < 0.0001, unpaired t -test. (c) Quantification of IGF-1 concentration in regenerated aortas 30 and 90 days after graft implantation in WT and Apoe −/− rats. ∗∗ indicates p < 0.01, Tukey's post-hoc test. For each time point and each group, five different samples from five different animals were analyzed (n = 5). UMAP of fibroblasts in regenerated aortas 30 days (d) and 90 days (e) after graft implantation in WT and Apoe −/− rats, heatmap of cell cycle (Ccnd1, Ccnd2, and Ccnd3) scores in UMAP of fibroblasts, and box plots of cell cycle scores in fibroblasts. ∗∗∗∗ indicates p < 0.0001, unpaired t -test. (f) Immunofluorescence staining of Ki67 in regenerated aortas 30 and 90 days after graft implantation in WT and Apoe −/− rats. L indicates lumens. (g) Quantification of Ki67 positive cells in regenerated aortas. ∗∗ indicates p < 0.01, Tukey's post-hoc test. For each time point and each group, five different images from five different animals were analyzed (n = 5). (h) Quantification of IGF-1 in culture mediums of WT and APOE KO macrophages after their culture on PCL scaffolds for 48 h by ELISA. ∗∗ indicates p < 0.01, unpaired t -test. For each group, three different samples were analyzed (n = 3). (i) Immunofluorescence staining of Ki67 in WT and APOE KO fibroblasts after treatment with IGF-1 (10 ng/mL) for 24 h. Cells were counterstained with phalloidin. (j) Quantification of proliferation of WT and APOE KO fibroblasts treated with IGF-1 (10 ng/mL) for 24 h using cell counting kit-8 (CCK-8). ∗∗ indicates p < 0.01, Tukey's post-hoc test. For each group, three different samples were analyzed (n = 3). (k) Quantification of proliferation of WT fibroblasts treated with conditioned medium (CM) with or without IGF-1 blocking antibody (Ab, 1 μg/mL) for 24 h using CCK-8. CM were medium conditioned by WT macrophages cultured on PCL scaffolds for 48 h ∗∗ indicates p < 0.01, Tukey's post-hoc test. For each group, three different samples were analyzed (n = 3).

Article Snippet: Exogenous APOE (0.25 μg/mL, MCE, HY-P701096), TGF-β1 (10 ng/mL, MCE, HY-P7117), IGF-1 (10 ng/mL, MCE), conditioned medium by macrophages, or IGF-1 blocking antibody (1 μg/mL, Invitrogen, MA5-18035) was added into culture medium and incubated with WT or APOE KO fibroblasts for 24 h.

Techniques: Expressing, Concentration Assay, Immunofluorescence, Staining, Enzyme-linked Immunosorbent Assay, Cell Counting, CCK-8 Assay, Blocking Assay, Cell Culture

Journal: Bioactive Materials

Article Title: Apolipoprotein E knockout attenuates vascular graft fibrosis by reducing profibrotic macrophage formation through low-density lipoprotein receptor related protein 1

doi: 10.1016/j.bioactmat.2026.01.029

Figure Lengend Snippet: Downregulation of APOE by AAV ameliorating fibrosis during vascular regeneration after graft implantation in vivo . (a) Illustration of a strategy of adventitial delivery of AAV-shRNA(Apoe) to inhibit APOE levels in regenerated aortas after graft implantation in vivo . Two weeks after graft implantation in vivo , AAV-shRNA(Apoe) were injected into the adventitia of the regenerated aortas, which were then harvested for analysis three weeks later. (b) M mode images of ultrasound detection of regenerated aortas treated with PBS, AAV-shRNA(NC), and AAV-shRNA(Apoe) for 3 weeks. Arrow heads indicate movement of vascular walls. (c) Tensile tests of regenerated aortas treated with PBS, AAV-shRNA(NC), and AAV-shRNA(Apoe) for 3 weeks. (d) Quantification of RI, PI, and compliance of regenerated aortas treated with PBS, AAV-shRNA(NC), and AAV-shRNA(Apoe) for 3 weeks. ∗∗ indicates p < 0.01, Tukey's post-hoc test. For each group, six different images from six different animals were analyzed (n = 6). (e) Quantification of elastic modulus of regenerated aortas treated with PBS, AAV-shRNA(NC), and AAV-shRNA(Apoe) for 3 weeks. ∗∗ indicates p < 0.01, Tukey's post-hoc test. For each group, six different images from six different animals were analyzed (n = 6). (f) H&E, MTC and EVG staining of regenerated aortas treated with PBS, AAV-shRNA(NC), and AAV-shRNA(Apoe) for 3 weeks. (g) Immunofluorescence staining of COL I, COL III, elastin, αSMA, and eNOS in regenerated aortas treated with PBS, AAV-shRNA(NC), and AAV-shRNA(Apoe) for 3 weeks. L indicates lumens. Arrow heads indicate capillaries. Quantification of adventitia thickness (h), collagen positive areas according to MTC staining (i), elastin positive areas according to EVG staining (j), COL I positive areas (k), COL III positive areas (l), and number of capillaries (m) in adventitial areas of regenerated aortas. (n) Immunofluorescence staining of CTSD and CD68 in regenerated aortas treated with PBS, AAV-shRNA(NC), and AAV-shRNA(Apoe) for 3 weeks. (o) CD68 and CTSD double positive cells in regenerated aortas. ∗∗ indicates p < 0.01, Tukey's post-hoc test. For each group, six different samples from six different animals were analyzed (n = 6). (p) WB results of APOE, CTSD and SPP1 levels in regenerated aortas treated with PBS, AAV-shRNA(NC), and AAV-shRNA(Apoe) for 3 weeks and quantification of levels of APOE, CTSD and SPP1 in regenerated aortas. ∗∗ indicates p < 0.01, Tukey's post-hoc test. For each group, six different samples from six different animals were analyzed (n = 6). (q) Quantification of IGF-1 concentrations in regenerated aortas treated with PBS, AAV-shRNA(NC), and AAV-shRNA(Apoe) for 3 weeks by ELISA. ∗∗ indicates p < 0.01, Tukey's post-hoc test. For each group, six different samples from six different animals were analyzed (n = 3).

Article Snippet: Exogenous APOE (0.25 μg/mL, MCE, HY-P701096), TGF-β1 (10 ng/mL, MCE, HY-P7117), IGF-1 (10 ng/mL, MCE), conditioned medium by macrophages, or IGF-1 blocking antibody (1 μg/mL, Invitrogen, MA5-18035) was added into culture medium and incubated with WT or APOE KO fibroblasts for 24 h.

Techniques: In Vivo, shRNA, Injection, Staining, Immunofluorescence, Enzyme-linked Immunosorbent Assay

Journal: bioRxiv

Article Title: XL-MS and De Novo Protein Design Identified a Common Motif for TREM2 Binding

doi: 10.64898/2026.04.23.720433

Figure Lengend Snippet: (a) SDS-PAGE analysis showing successful cross-linking of the heterodimeric TREM2 ECD /Trx-ApoE3 complex. (b) Representative high-quality MS/MS spectra of inter-protein cross-linked peptides. (c) Bar representation showing intra-protein XLs, inter-protein XLs, and inter-protein self-links. Figure was created using xiNET . ApoE3: light blue (N-terminal region, residues 1-167), light yellow (hinge region, residues 168-205), and pink (C-terminal region, residues 206-299).

Article Snippet: 20 μM Trx-ApoE3 (Sino Biological 10817-H30E) and 20 μM TREM2 ectodomain were incubated for 1 h at 4°C.

Techniques: SDS Page, Tandem Mass Spectroscopy

Journal: bioRxiv

Article Title: XL-MS and De Novo Protein Design Identified a Common Motif for TREM2 Binding

doi: 10.64898/2026.04.23.720433

Figure Lengend Snippet: (a) Mapping intra-ApoE3 cross-links onto the NMR structure (pdb 2L7B). Red line: incompatible XLs with Cβ-Cβ solvent accessible surface distance (SASD) > 35 Å. Blue line: compatible XLs. (b) Filtering the structure ensemble of ApoE3 (Protein Ensemble Database PED07094) by intra-ApoE3 XLs yielded Model 49 with the highest structural compatibility. (c) The best-scoring model of TREM2/ApoE3 complex generated using Haddock. (d) Zoom-in view of the binding interface. ApoE3: light blue (N-terminal region, residues 1-167), light yellow (hinge region, residues 168-205), and pink (C-terminal region, residues 206-299). TREM2 ECD : CDR1(residue 40-42), CDR2(residue 69-72), and CDR3 (residue 88-91).

Article Snippet: 20 μM Trx-ApoE3 (Sino Biological 10817-H30E) and 20 μM TREM2 ectodomain were incubated for 1 h at 4°C.

Techniques: Solvent, Generated, Binding Assay, Residue

Journal: bioRxiv

Article Title: XL-MS and De Novo Protein Design Identified a Common Motif for TREM2 Binding

doi: 10.64898/2026.04.23.720433

Figure Lengend Snippet: (a-m) Design models of mini-proteins in complex with TREM2 ECD (left) and binding affinity determined by microscale thermophoresis (right). Numbers in brackets represent the 68.3% confidence interval calculated by “error-surface projection” .

Article Snippet: 20 μM Trx-ApoE3 (Sino Biological 10817-H30E) and 20 μM TREM2 ectodomain were incubated for 1 h at 4°C.

Techniques: Binding Assay, Microscale Thermophoresis

Journal: bioRxiv

Article Title: XL-MS and De Novo Protein Design Identified a Common Motif for TREM2 Binding

doi: 10.64898/2026.04.23.720433

Figure Lengend Snippet: (a) SDS-PAGE analysis showing successful cross-linking of the heterodimeric TREM2 ECD /Trx-ApoE3 complex. (b) Representative high-quality MS/MS spectra of inter-protein cross-linked peptides. (c) Bar representation showing intra-protein XLs, inter-protein XLs, and inter-protein self-links. Figure was created using xiNET . ApoE3: light blue (N-terminal region, residues 1-167), light yellow (hinge region, residues 168-205), and pink (C-terminal region, residues 206-299).

Article Snippet: 20 μM Trx-ApoE3 (Sino Biological 10817-H30E) and 20 μM TREM2 ectodomain were incubated for 1 h at 4°C.

Techniques: SDS Page, Tandem Mass Spectroscopy

Journal: bioRxiv

Article Title: PRINCIPLES GOVERNING ENDOTHELIAL CAVEOLAE ORGANIZATION DURING ANGIOGENESIS

doi: 10.64898/2026.03.27.714916

Figure Lengend Snippet: (A) Representative images of circle micropatterns with cell-repulsive Lipidure (magenta) and extracellular matrix (ECM) protein fibronectin (green). Scale bars indicate 100µm (10x & 20x) and 10µm for the 60x image. (B) Representative images of endothelial cells stained for Caveolin-1 (Cav1, green), F-actin (red), and DNA (blue) on circle patterns. (C) Average cell projection (left), quartile probability map (middle), and radial density map (right) of indicated groups. Intensity and color scales are displayed at the bottom. N= number of cells. (D) Cartoon to view the process of distance vs. intensity plotting. (E) Distance vs. intensity graph for indicated groups. Distances are calculated and normalized from the edge (0) to the center (1); intensities are also normalized. N=number of points. Interpolated graphs (right panels) show mean line (dark blue) and standard deviation (light blue). (F) Cartoon to view the process of distance vs. intensity plotting. (G) X-Z view average models for indicated groups. N= number of cells. (H) 3-dimensional renderings of Cav1 (top, green), F-actin (middle, red), and a merge including labeled DNA (bottom, blue) from both a 3D (left) and X-Z (right) point of view. (I) Transmission Electron Microscopy (TEM) representative images depicting in regions of interest. In the Caveolae row, scale bars indicate 10 µm (left 2) 1µm (middle, 3), 500 nm (4), and 200 nm (rightmost, 5). In the Lamella row, scale bars indicate 1 µm.

Article Snippet: Images were captured using a Nikon Plan Apo 60x NA 1.40 oil objective using Olympus type F immersion oil NA 1.518, Nikon Apo LWD 20x NA 0.95 or Nikon Apo LWD 40x NA 1.15 water objective.

Techniques: Staining, Standard Deviation, Labeling, Transmission Assay, Electron Microscopy