Journal: BMC Genomics

Article Title: Molecular adaptations in MMP genes support lung elasticity and diving adaptations in cetaceans

doi: 10.1186/s12864-025-11751-2

Figure Lengend Snippet: Regression analysis of gene evolution rates with maximum diving depth and time. ( A ) Regression of maximum diving depth against the evolution rate of MMP16 ( R ²=0.2408, P = 0.01186); ( B ) Regression of maximum diving time against the evolution rate of MMP16 ( R² =0.3057, P = 0.00448); ( C ) Regression of maximum diving depth against the evolution rate of MMP9 ( R 2 = 0.3381, P = 0.00268). ( D ) Regression of maximum diving depth against the evolution rate of MMP25 ( R 2 = 0.2026, P = 0.02045); ( E ) Regression of maximum diving depth against the evolution rate of MMP17 ( R 2 = 0.3316, P = 0.00298);( F ) Regression of maximum diving depth against the evolution rate of MMP11 ( R 2 = 0.3120, P = 0.00406)

Article Snippet: The following antibodies were used in the study: Anti- MMP9 (Cat No. #27306-1-AP), Collagen I (Cat No. #14695-1-AP), GAPDH (Cat No. #10494-1-AP), HA (Cat No. #51064-2-AP), and HRP-conjugated Goat Anti-Rabbit IgG (H + L) (Cat No. #SA00001-2), all purchased from Proteintech Group (Wuhan, China).

Techniques:

Journal: BMC Genomics

Article Title: Molecular adaptations in MMP genes support lung elasticity and diving adaptations in cetaceans

doi: 10.1186/s12864-025-11751-2

Figure Lengend Snippet: MMP9 overexpression, protein modifications, and collagen degradation. ( A ) The highest XCorr protein spectrum peak identified from the overexpression of T. truncatus MMP9 . ( B ) In cetaceans, the specific amino acid sites of MMP9 undergo post-translational modifications: the 319 S site is modified with HexNAc, the 532 S site is modified with Phospho and HexNAc, the 661 M site is modified with Oxidation, and the 568 S site is modified with Phospho and HexNAc. ( C ) The highest XCorr protein spectrum peak identified from the overexpression of B. taurus MMP9 . ( D ) Collagen I degradation ability of T. truncatus and B. taurus MMP9 overexpressed in A549 cells. The blots/gels displayed in the figure represent cropped versions. Full-length blots/gels are presented in Fig

Article Snippet: The following antibodies were used in the study: Anti- MMP9 (Cat No. #27306-1-AP), Collagen I (Cat No. #14695-1-AP), GAPDH (Cat No. #10494-1-AP), HA (Cat No. #51064-2-AP), and HRP-conjugated Goat Anti-Rabbit IgG (H + L) (Cat No. #SA00001-2), all purchased from Proteintech Group (Wuhan, China).

Techniques: Over Expression, Modification

Journal: BMC Genomics

Article Title: Molecular adaptations in MMP genes support lung elasticity and diving adaptations in cetaceans

doi: 10.1186/s12864-025-11751-2

Figure Lengend Snippet: Migration ability of A549 cells after MMP9 overexpression. ( A ) Wound healing status after 0–24 h of overexpression of T. truncatus and B. taurus genes. ( B ) Quantitative analysis of wound healing rate, ns: Not significant; *: P < 0.05; **: P < 0.01; ***: P < 0.001; ***: P < 0.0001. P value of 12 h (Tur&Bos; Tur&NC; Bos&NC: 0.0059; 0.0022; 0.0098); P value of 24 h (Tur&Bos; Tur&NC; Bos&NC: 0.0241; 0.001; 0.001)

Article Snippet: The following antibodies were used in the study: Anti- MMP9 (Cat No. #27306-1-AP), Collagen I (Cat No. #14695-1-AP), GAPDH (Cat No. #10494-1-AP), HA (Cat No. #51064-2-AP), and HRP-conjugated Goat Anti-Rabbit IgG (H + L) (Cat No. #SA00001-2), all purchased from Proteintech Group (Wuhan, China).

Techniques: Migration, Over Expression

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Targeting ICAM1 through LIF-mediated NF-κB/JAK2-STAT3 crosstalk protects nucleus pulposus from IL-1β-driven pyroptosis to ameliorate intervertebral disc degeneration

doi: 10.1186/s13018-025-06494-5

Figure Lengend Snippet: Expression of LIF and ICAM1 in human IVD tissues with varying degrees of degeneration. A Representative MRI images of human discs classified as Pfirrmann grades II, III, and V. B – C H&E and Safranin O–Fast Green staining of degenerated human discs (original magnification 20×, scale bar = 100 μm). D RT-qPCR analysis of mRNA levels of LIF, MMP13, Col II, IL-1β, and ICAM1 in discs of varying degeneration severity; gene expression was calculated using the 2 –ΔΔCt method. E – F Western blot and quantitative analysis of LIF, MMP13, Col II, IL-1β, and ICAM1 protein expression. G – H IHC scoring and quantification of LIF, MMP13, Col II, IL-1β, and ICAM1. Data are presented as means ± SD from at least three independent experiments. Statistical significance is indicated as p < 0.05, p < 0.01, ## p < 0.001 compared to grade II

Article Snippet: After antigen retrieval and blocking with 5% normal goat serum, the sections were incubated with the following primary antibodies: LIF (1:100, Proteintech, 26757-1-AP), Collagen II (Col II) (1:200, ab34712, Abcam), MMP13 (1:200, Proteintech, 18165-1-AP), ICAM1 (1:100, Abcam, ab282575), IL-1β (1:200, Proteintech, 16806-1-AP), p-P65 (1:100, Immunoway, YP0188), and p-STAT3 (1:100, Immunoway, YP0251).

Techniques: Expressing, Staining, Quantitative RT-PCR, Gene Expression, Western Blot

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Targeting ICAM1 through LIF-mediated NF-κB/JAK2-STAT3 crosstalk protects nucleus pulposus from IL-1β-driven pyroptosis to ameliorate intervertebral disc degeneration

doi: 10.1186/s13018-025-06494-5

Figure Lengend Snippet: Expression of LIF and ICAM1 in NP cells and the rat IDD model. A Representative MRI images of rat IVDs two and four weeks after AF puncture. B – C H&E and Safranin O–Fast Green staining of rat discs post-puncture (original magnification 4× or 20×, scale bars = 200–100 μm). D Pfirrmann grading of rat IVDs post-puncture. E – F IF staining of MMP13, GSDMD, LIF, and ICAM1 in control and IDD model groups (scale bar = 100 μm). G – H Western blot analysis and quantification of MMP13, GSDMD, GSDMDN, LIF, and ICAM1 following IL-1β treatment at different concentrations. Data are presented as means ± SD from at least three independent experiments. Statistical significance is represented as p < 0.05, p < 0.01, ## p < 0.001 compared to control

Article Snippet: After antigen retrieval and blocking with 5% normal goat serum, the sections were incubated with the following primary antibodies: LIF (1:100, Proteintech, 26757-1-AP), Collagen II (Col II) (1:200, ab34712, Abcam), MMP13 (1:200, Proteintech, 18165-1-AP), ICAM1 (1:100, Abcam, ab282575), IL-1β (1:200, Proteintech, 16806-1-AP), p-P65 (1:100, Immunoway, YP0188), and p-STAT3 (1:100, Immunoway, YP0251).

Techniques: Expressing, Staining, Control, Western Blot

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Targeting ICAM1 through LIF-mediated NF-κB/JAK2-STAT3 crosstalk protects nucleus pulposus from IL-1β-driven pyroptosis to ameliorate intervertebral disc degeneration

doi: 10.1186/s13018-025-06494-5

Figure Lengend Snippet: LIF expression mitigates AF puncture-induced IDD in vivo. A Schematic of the in vivo experimental workflow. B Representative MRI images of rat IVDs across treatment groups. C H&E and Safranin O–Fast Green staining of rat discs (scale bars = 100 μm–20 μm). D Pfirrmann scores of rat discs in each group. E – F IHC staining and quantification of p-P65 and p-STAT3 protein levels. G – H IF staining and quantitative analysis of ICAM1, MMP13, NLRP3, and GSDMD (scale bars = 100 μm–20 μm). Data are presented as means ± SD from at least three independent experiments. Statistical significance is indicated as p < 0.05, p < 0.01, ## p < 0.001 compared to control

Article Snippet: After antigen retrieval and blocking with 5% normal goat serum, the sections were incubated with the following primary antibodies: LIF (1:100, Proteintech, 26757-1-AP), Collagen II (Col II) (1:200, ab34712, Abcam), MMP13 (1:200, Proteintech, 18165-1-AP), ICAM1 (1:100, Abcam, ab282575), IL-1β (1:200, Proteintech, 16806-1-AP), p-P65 (1:100, Immunoway, YP0188), and p-STAT3 (1:100, Immunoway, YP0251).

Techniques: Expressing, In Vivo, Staining, Immunohistochemistry, Control

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Targeting ICAM1 through LIF-mediated NF-κB/JAK2-STAT3 crosstalk protects nucleus pulposus from IL-1β-driven pyroptosis to ameliorate intervertebral disc degeneration

doi: 10.1186/s13018-025-06494-5

Figure Lengend Snippet: ICAM1 inhibition ameliorates AF puncture-induced IDD in vivo. A Schematic representation of the in vivo experimental workflow for rat models. B Representative MRI images of rat IVDs across experimental groups. C H&E and Safranin O–Fast Green staining of disc tissues in the various groups (scale bars = 100 μm–20 μm). D Pfirrmann grading scores of rat discs in each group. E – F Western blot analysis and quantification of MMP13, Col II, GSDMD, GSDMDN, and NLRP3 protein expression. G – I IF staining and quantitative analysis of Col II, MMP13, NLRP3, and GSDMD in the same groups (scale bars = 100 μm–20 μm). Data are presented as means ± standard deviation (SD) from a minimum of three independent experiments. Statistical significance is denoted as p < 0.05, p < 0.01, ## p < 0.001 compared to control

Article Snippet: After antigen retrieval and blocking with 5% normal goat serum, the sections were incubated with the following primary antibodies: LIF (1:100, Proteintech, 26757-1-AP), Collagen II (Col II) (1:200, ab34712, Abcam), MMP13 (1:200, Proteintech, 18165-1-AP), ICAM1 (1:100, Abcam, ab282575), IL-1β (1:200, Proteintech, 16806-1-AP), p-P65 (1:100, Immunoway, YP0188), and p-STAT3 (1:100, Immunoway, YP0251).

Techniques: Inhibition, In Vivo, Staining, Western Blot, Expressing, Standard Deviation, Control

Journal: Clinical and Translational Medicine

Article Title: Hypoxia‐induced secretory autophagy in cancer‐associated fibroblasts promotes ECM remodelling through serglycin secretion in oral squamous cell carcinoma

doi: 10.1002/ctm2.70556

Figure Lengend Snippet: CAFs secrete SRGN via autophagy to promote OSCC cell invasion and migration by facilitating ECM remodelling through interaction with MMP2/9. (A, B) WB analysis of SRGN protein expression levels and quantification in WT CAFs and SRGN KO CAFs. (C) qPCR analysis of SRGN gene expression in WT CAFs and SRGN KO CAFs. (D) UV image of the agarose gel. (E) The supernatant from normoxic and hypoxic WT CAFs, WT CAFs + 3‐MA, and SRGN KO CAFs was collected and co‐cultured with OSCC cells. Invasion ability was assessed by transwell assays. (F) Invasion cell numbers were quantified using ImageJ software. (* p < .05; ** p < .01; *** p < .001). (G) The supernatant from normoxic and hypoxic WT CAFs, WT CAFs + 3‐MA, and SRGN KO CAFs was collected and co‐cultured with SCC9 cells. Migration ability was assessed by scratch assays. (H) Prediction of SRGN‐binding proteins using the STRING database. (I) HEK293T cells were transfected with SRGN‐Flag and incubated for 48 h. Cell lysates were incubated with anti‐Flag beads, and immunoblotting (IB) was performed using anti‐Flag, anti‐MMP11, anti‐MMP9, and anti‐MMP2 antibodies. (J) WB analysis of changes in MMP9, MMP11, MMP2, and SRGN protein expression levels in WT CAFs and SRGN KO CAFs. (K) Gelatin degradation assays were performed to evaluate gelatin degradation after 24 h of co‐culture of CAL27 cells with the supernatants from normoxic and hypoxic WT CAFs, WT CAFs + 3‐MA, and SRGN KO CAFs. Scale bar = 20 µm.

Article Snippet: Primary antibodies used in this assay included: β‐actin (1:4000, 20536‐1, Proteintech), MMP9 (1:1000, bs‐4593R, Bioss), MMP2 (1:1000, CY5189, Abways), MMP11 (1:1000, CY5778, Abways), Flag (1:5000, 80801‐2‐RR, Proteintech).

Techniques: Migration, Expressing, Gene Expression, Agarose Gel Electrophoresis, Cell Culture, Software, Binding Assay, Transfection, Incubation, Western Blot, Co-Culture Assay

Journal: Clinical and Translational Medicine

Article Title: Hypoxia‐induced secretory autophagy in cancer‐associated fibroblasts promotes ECM remodelling through serglycin secretion in oral squamous cell carcinoma

doi: 10.1002/ctm2.70556

Figure Lengend Snippet: CAF‐derived SRGN promotes tumour invasion and ECM degradation via autophagy secretion. (A) In vivo xenograft models were established in nude mice and divided into four groups: (a) CAL27, (b) CAL27 + WT CAFs, (c) CAL27 + WT CAFs (3‐MA), and (d) CAL27 + SRGN KO CAFs. (B) Tumour volume and tumour weight were monitored ( n = 7). (C, D) H&E staining and IHC analysis of COL1, E‐cadherin, MMP2 and MMP9 were performed in orthotopic xenograft tumour tissues. The expression levels of COL1, E‐cadherin, MMP2 and MMP9 were quantitatively analyzed using Fiji software. Scale bar = 100 µm. (* p < .05; ** p < .01; *** p < .001).

Article Snippet: Primary antibodies used in this assay included: β‐actin (1:4000, 20536‐1, Proteintech), MMP9 (1:1000, bs‐4593R, Bioss), MMP2 (1:1000, CY5189, Abways), MMP11 (1:1000, CY5778, Abways), Flag (1:5000, 80801‐2‐RR, Proteintech).

Techniques: Derivative Assay, In Vivo, Staining, Expressing, Software

Journal: Clinical and Translational Medicine

Article Title: Hypoxia‐induced secretory autophagy in cancer‐associated fibroblasts promotes ECM remodelling through serglycin secretion in oral squamous cell carcinoma

doi: 10.1002/ctm2.70556

Figure Lengend Snippet: Mechanism diagram of hypoxic CAFs‐derived SRGN secretion and tumour progression promotion. Under normal conditions, SRGN is translocated into the ER and subsequently transported via the Golgi apparatus for secretion into the extracellular space. Under hypoxic conditions, elevated autophagy levels in CAFs facilitate the release of SRGN into the ECM through secretory autophagy‐mediated plasma membrane fusion. Within the ECM, SRGN interacts with MMP2 and MMP9, enhancing ECM remodelling and ultimately promoting the invasive capacity of OSCC cells.

Article Snippet: Primary antibodies used in this assay included: β‐actin (1:4000, 20536‐1, Proteintech), MMP9 (1:1000, bs‐4593R, Bioss), MMP2 (1:1000, CY5189, Abways), MMP11 (1:1000, CY5778, Abways), Flag (1:5000, 80801‐2‐RR, Proteintech).

Techniques: Derivative Assay, Clinical Proteomics, Membrane

Journal: Molecular medicine reports

Article Title: lncRNA FEZF1‑AS1 promotes migration, invasion and epithelial‑mesenchymal transition of retinoblastoma cells by targeting miR‑1236‑3p.

doi: 10.3892/mmr.2020.11478

Figure Lengend Snippet: Figure 3. Epithelial‑mesenchymal transition of retinoblastoma cells is suppressed by shRNA‑FEZF1‑AS1. Western blotting was used to analyze the protein expression levels of (A) Vimentin, Snail, Slug and β‑catenin, (B) N‑cadherin, E‑cadherin, Claudin‑1 and (C) MMP2 and MMP9 in Y79 cells transfected with shRNA‑NC or shRNA‑FEZF1‑AS1. All data are expressed as the mean ± SEM. **P<0.01, ***P<0.001 vs. shRNA‑NC group. FEZF1‑AS1, FEZ family zinc finger 1 antisense RNA 1; shRNA, short hairpin RNA; NC, negative control; MMP, matrix metalloproteinase.

Article Snippet: The membranes were then incubated with the following primary antibodies at 4 ̊C overnight: Anti‐Vimentin (1:1,000; cat. no. 3932; Cell Signaling Technology, Inc.), anti‐Snail (1:1,000; cat. no. 3879; Cell Signaling Technology, Inc.), anti‐Slug (1:1,000; cat. no. 9585; Cell Signaling Technology, Inc.), anti‐Claudin‐1 (1:1,000; cat. no. 4933; Cell Signaling Technology, Inc.), anti‐β-catenin (1:500; cat. no. sc‐59737; Santa Cruz Biotechnology, Inc.), anti‐N‐cadherin (1:500; cat. no. sc‐59987; Santa Cruz Biotechnology, Inc.), anti‐E‐cadherin (1:500; cat. no. sc‐8426; Santa Cruz Biotechnology, Inc.), anti‐matrix metalloproteinase (MMP) 2 (1:1,000; cat. no. 10373‐2‐AP; ProteinTech Group, Inc.), anti‐MMP9 (1:1,000; cat. no. 10375‐2‐AP; ProteinTech Group, Inc.) and anti‐GAPDH (1:1,000; cat. no. SAB5600208; Sigma-aldrich; Merck KGaa).

Techniques: Western Blot, Expressing, Transfection, shRNA, Negative Control

Journal: Molecular medicine reports

Article Title: lncRNA FEZF1‑AS1 promotes migration, invasion and epithelial‑mesenchymal transition of retinoblastoma cells by targeting miR‑1236‑3p.

doi: 10.3892/mmr.2020.11478

Figure Lengend Snippet: Figure 6. Continued. Inhibition of miR‑1236‑3p reverses the effects of shRNA‑FEZF1‑AS1 on epithelial‑mesenchymal transition. (A) Western blotting was used to analyze the protein expression levels of (A) Vimentin, Snail, Slug and β‑catenin, (B) N‑cadherin, E‑cadherin and Claudin‑1, and (C) MMP2 and MMP9 in Y79 cells transfected with shRNA‑NC or shRNA‑FEZF1‑AS1 with or without miR‑1236‑3p inhibitor or miR‑NC inhibitor. All data are expressed as the mean ± SEM. ***P<0.001 vs. shRNA‑NC group; #P<0.05, ##P<0.01, ###P<0.001 vs. shRNA‑FEZF1‑AS1 + miR‑NC inhibitor group. FEZF1‑AS1, FEZ family zinc finger 1 antisense RNA 1; shRNA, short hairpin RNA; NC, negative control; miR, microRNA; MMP, matrix metalloproteinase.

Article Snippet: The membranes were then incubated with the following primary antibodies at 4 ̊C overnight: Anti‐Vimentin (1:1,000; cat. no. 3932; Cell Signaling Technology, Inc.), anti‐Snail (1:1,000; cat. no. 3879; Cell Signaling Technology, Inc.), anti‐Slug (1:1,000; cat. no. 9585; Cell Signaling Technology, Inc.), anti‐Claudin‐1 (1:1,000; cat. no. 4933; Cell Signaling Technology, Inc.), anti‐β-catenin (1:500; cat. no. sc‐59737; Santa Cruz Biotechnology, Inc.), anti‐N‐cadherin (1:500; cat. no. sc‐59987; Santa Cruz Biotechnology, Inc.), anti‐E‐cadherin (1:500; cat. no. sc‐8426; Santa Cruz Biotechnology, Inc.), anti‐matrix metalloproteinase (MMP) 2 (1:1,000; cat. no. 10373‐2‐AP; ProteinTech Group, Inc.), anti‐MMP9 (1:1,000; cat. no. 10375‐2‐AP; ProteinTech Group, Inc.) and anti‐GAPDH (1:1,000; cat. no. SAB5600208; Sigma-aldrich; Merck KGaa).

Techniques: Inhibition, Western Blot, Expressing, Transfection, shRNA, Negative Control

Journal: Cytokine

Article Title: IL-33/ST2 enhances MMP-12 expression by macrophages to mediate inflammatory and immune response in IgG4-Related Ophthalmic Disease.

doi: 10.1016/j.cyto.2024.156754

Figure Lengend Snippet: Fig. 2. Expression of IL-33/ST2 in IgG4-ROD A: Immunohistochemistry anal- ysis of IL-33、ST2 in IgG4-ROD lacrimal gland tissues relative to normal tissues. B: Statistical analysis of the immunohistochemistry results from 9 IgG4-ROD patients with lacrimal gland involvement and 9 normal lacrimal gland tis- sues. Normal: lacrimal gland prolapse patients. (*, p < 0.05).

Article Snippet: Antibodies used for immunohistochemical analysis included IL-33 (Proteintech, Catalog no.: 66235–1-Ig), ST2 (Proteintech, Catalog no.: 60112–1-Ig), and MMP-12 (Proteintech, Catalog no.: 66930–1-Ig).

Techniques: Expressing, Immunohistochemistry