timp 3  (R&D Systems)

Journal: Frontiers in Immunology

Article Title: Exploratory transcriptomic analysis of mouse articular cartilage in response to tissue inhibitor of metalloproteinase 3 identifies inflammation-associated gene expression changes

doi: 10.3389/fimmu.2026.1794078

Figure Lengend Snippet: Experimental design. Femoral head articular cartilage samples from 16 mice were harvested in pairs and each pair was placed in one well of a 96-well plate with serum-free Opti-MEM supplemented with 1% penicillin-streptomycin, maintained under standard normoxic conditions (21% O 2 , 5% CO 2 , 37°C). After three days, half of the cultures were transferred to a hypoxia incubator (3% O 2 ). Following 24 hours of normoxic or hypoxic incubation, cultures were treated with recombinant human TIMP-3 (100 nM; 2.6 µg/ml) or vehicle for 20 hours, and RNA was extracted for RNA sequencing (n = 4 per group). Group labels: NC, normoxia control; NT, normoxia TIMP-3; HC, hypoxia control; HT, hypoxia TIMP-3.

Article Snippet: After 24 hours, cultures were treated with recombinant human TIMP-3 (R&D Systems, Abingdon, Oxon, UK) at 100 nM, (2.6 μg/ml) or vehicle control for 20 hours under normoxia or hypoxia.

Techniques: Incubation, Recombinant, RNA Sequencing, Control

Journal: Frontiers in Immunology

Article Title: Exploratory transcriptomic analysis of mouse articular cartilage in response to tissue inhibitor of metalloproteinase 3 identifies inflammation-associated gene expression changes

doi: 10.3389/fimmu.2026.1794078

Figure Lengend Snippet: TIMP-3 upregulates Saa3 gene expression in cartilage under normoxia and hypoxia. Articular cartilage explants were cultured and processed for RNA-seq as described in the legend to Table 2 . (A) Venn diagram showing overlap of genes differentially regulated in response to TIMP-3 under normoxia (Norm; 21% O 2 ) and hypoxia (Hyp; 3% O 2 ). (B) RT-qPCR validation of Saa3 . RNA-seq (left) and RT-qPCR (right) data shown as log 2 FC versus the mean of the controls (mean ± SD, n = 4). RNA-seq: log 2 FC were calculated from normalized CPM values; § FDR < 0.05 (hypoxia effect), # P < 0.01 (TIMP-3 effect) by quasi-likelihood F-test applied to raw counts (edgeR). RT-qPCR: *P < 0.05 by unpaired two-sided Welch’s t-test on log 2 FC values (-ΔΔCq). Ctrl, control; FC, fold change.

Article Snippet: After 24 hours, cultures were treated with recombinant human TIMP-3 (R&D Systems, Abingdon, Oxon, UK) at 100 nM, (2.6 μg/ml) or vehicle control for 20 hours under normoxia or hypoxia.

Techniques: Gene Expression, Cell Culture, RNA Sequencing, Quantitative RT-PCR, Biomarker Discovery, Control

Journal: Frontiers in Immunology

Article Title: Exploratory transcriptomic analysis of mouse articular cartilage in response to tissue inhibitor of metalloproteinase 3 identifies inflammation-associated gene expression changes

doi: 10.3389/fimmu.2026.1794078

Figure Lengend Snippet: RNA-seq analysis of TIMP-3–treated cartilage under normoxia. (A) MA plot showing differential expression between TIMP-3–treated and control samples, with log 2 FC plotted against average log 2 CPM expression (n = 4). Grey: no change, red: upregulated, blue: downregulated transcripts (P < 0.01 by quasi-likelihood F-test in edgeR, |log 2 FC| > 0.58). The 10 most highly expressed regulated genes are labelled. Complete gene lists are in . (B) Heatmap of differentially expressed genes (log 2 FC versus the mean of the controls). Genes are ordered by hierarchical clustering. Sample labels: NC1-4: normoxia controls; NT1-4: normoxia TIMP-3–treated. (C) Sole significantly enriched pathway (FDR < 0.05) from DAVID analysis of 26 upregulated genes. As only one KEGG pathway passed the significance threshold, it is shown individually together with its enrichment score (Fold enrichment) and FDR for visual consistency within the multipanel figure. (D) RT-qPCR validation. RNA-seq (left) and RT-qPCR (right) data shown as log 2 FC versus the mean of the controls (mean ± SD, n = 4). RNA-seq: log 2 FC were calculated from normalized CPM values; § FDR < 0.05 (hypoxia effect), # P < 0.01 (TIMP-3 effect) by quasi-likelihood F-test applied to raw counts (edgeR). RT-qPCR: *P < 0.05, **P < 0.01, ***P < 0.001 by unpaired two-sided Welch’s t-test on log 2 FC values (-ΔΔCq). CPM, counts per million; Ctrl, control; FC, fold change; Norm, normoxia; Hyp, hypoxia.

Article Snippet: After 24 hours, cultures were treated with recombinant human TIMP-3 (R&D Systems, Abingdon, Oxon, UK) at 100 nM, (2.6 μg/ml) or vehicle control for 20 hours under normoxia or hypoxia.

Techniques: RNA Sequencing, Quantitative Proteomics, Control, Expressing, Quantitative RT-PCR, Biomarker Discovery

Journal: Frontiers in Immunology

Article Title: Exploratory transcriptomic analysis of mouse articular cartilage in response to tissue inhibitor of metalloproteinase 3 identifies inflammation-associated gene expression changes

doi: 10.3389/fimmu.2026.1794078

Figure Lengend Snippet: RNA-seq analysis of TIMP-3–treated cartilage under hypoxia. (A) MA plot showing differential expression between TIMP-3–treated and control articular cartilage, with log 2 FC plotted against average log 2 CPM expression (n = 4). Grey: no change, red: upregulated, blue: downregulated (P < 0.01, |log 2 FC| > 0.58). The 10 most highly expressed regulated genes are labelled. G1 and G2 correspond to E430024I08Rik and AC127578.1 respectively. Complete gene lists are in . (B) Heatmap of differentially expressed genes (log 2 FC versus the mean of the controls). Genes are ordered by hierarchical clustering. Sample labels: HC1-4: hypoxia controls; HT1-4: hypoxia TIMP-3-treated. (C) Protein–protein interaction (PPI) network corresponding to genes downregulated by TIMP-3 under hypoxia (P <0.01 by quasi-likelihood F-test in edgeR, |log 2 FC| > 0.58), generated using STRING (default interaction score ≥ 0.400). All nodes represent the initially filtered gene list and are included to show the network context and highlight that only Pbk and Racgap1 display a documented interaction. Line colors indicate evidence type: green, text mining; pink, experimental; black, co-expression. Combined interaction score: 0.711. (D) RT-qPCR validation. RNA-seq (left) and RT-qPCR (right) data shown as log 2 FC versus the mean of the controls (mean ± SD, n = 4). RNA-seq: log 2 FC were calculated from normalized CPM values; § FDR < 0.05 (hypoxia effect), # P < 0.01 (TIMP-3 effect) by quasi-likelihood F-test applied to raw counts (edgeR); RT-qPCR: *P < 0.05, **P < 0.01 by unpaired two-sided Welch’s t-test on log 2 FC values (-ΔΔCq). CPM, counts per million; Ctrl, control.

Article Snippet: After 24 hours, cultures were treated with recombinant human TIMP-3 (R&D Systems, Abingdon, Oxon, UK) at 100 nM, (2.6 μg/ml) or vehicle control for 20 hours under normoxia or hypoxia.

Techniques: RNA Sequencing, Quantitative Proteomics, Control, Expressing, Generated, Quantitative RT-PCR, Biomarker Discovery

Journal: Platelets

Article Title: Transcriptomic and functional characterization of megakaryocytic-derived platelet-like particles: impaired aggregation and prominent anti-tumor effects.

doi: 10.1080/09537104.2024.2449344

Figure Lengend Snippet: Figure 7. Signaling axes promoting or inhibiting oncogenicity. (A) Schematic representation of potential signaling axes mediating platelet-PCa pro- oncogenic interactions and PLP-PCa anti-oncogenic interactions. (B) RNA-seq expression values in TPMs of components in the platelet-PCa cell signaling axes. (C) RNA-seq expression values of components in the PLP-PCa cell signaling axes. Data in (B) and (C) presented as the mean ± SEM of n = 44 for platelets and n = 8 independent determinations for PLPs (determinations for MEG-01- and K-562-derived PLPs combined). RNA-Seq TPM values for MDA and RC77 were from a single determination. Statistical analysis was performed using a t-test (*p < .05). (D) Far left panel depicts relative 48-hour matrigel invasion by MDA-PCa-2b (MDA) and RC77T/E (RC77) cells incubated with vehicle (veh) + 5 ug/ml IgG isotype control, PLP + IgG, or PLP + 5 ug/ml neutralizing antibody against TIMP3 (β-TIMP3). Middle panel depicts relative 24-hour caspase activity in MDA and RC77 cells incubated with vehicle (veh) + 5 ug/ml IgG isotype control, PLP + IgG, or PLP + 5 ug/ml neutralizing antibody α-vegfb. Far right panel depicts relative 24-hour caspase activity in MDA cells incubated with conditioned medium (CM) derived from 24-hour culturing of MEG-01 PLPs (CM1), PCa cells + PLPs (CM2), and PCa cells + PLPs + platelets (CM3). Closed and open bars indicate incubation with 5 ug/ml IgG or α-TIMP3, respectively. Cell:PLP ratio was 1:500 and Cell:PLP:platelet ratio was 1:500:500 for all experiments. Data presented as the mean ± SEM of n = 4 independent determinations and analyzed by ANOVA and Dunnett’s post-hoc test. *significantly different (p < .05) compared to corresponding control (veh-containing group). #Significantly different (p < .05) compared to corresponding IgG group. Abbreviations: RC77, RC77T/E; MDA, MDA-PCa -2b; ITGA2B, integrin alpha 2b; ITGB3, integrin beta 3; FN1, fibronectin 1; IL32, interleukin 32; EGF, epidermal growth factor; TGFA, transforming growth factor alpha; EGFR, epidermal growth factor receptor; HER2, human epidermal growth factor receptor 2; ERBB3, human epidermal growth factor receptor 3; EPHA, EPH receptor A; EFNA, ephrin A; TIMP3, tissue inhibitor of metalloproteinases 3; MMP15, matrix metalloproteinase 15; VEGFB, vascular endothelial growth factor B; FGFR1, fibroblast growth factor receptor 1; IGFBP4, insulin-like growth factor-binding protein 4; LPR6, low-density lipoprotein receptor-related protein 6.

Article Snippet: Cells alone included an isotype IgG control (5 μg/ mL), and cells with PLPs were incubated with isotype IgG control (5 μg/ml) or a neutralizing antibody against TIMP3 (5 μg/ml; R&D Systems, Cat #MAB973-SP) or VEGFB (5 μg/ml; R&D Systems, Cat #MAB3372).

Techniques: RNA Sequencing, Expressing, Derivative Assay, Incubation, Control, Activity Assay, Binding Assay

Journal: eLife

Article Title: Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation

doi: 10.7554/eLife.87517

Figure Lengend Snippet:

Article Snippet: ELISA measurements were made using the Human TIMP-3 ELISA Kit from Invitrogen (Catalog # EH458RB) and precisely following the manufacturer’s instructions.

Techniques: Software, Sequencing, Enzyme-linked Immunosorbent Assay