mmp9  (Elabscience Biotechnology)

Journal: The EMBO Journal

Article Title: TRPML1 suppresses pulmonary fibrosis by limiting collagen and elastin deposition

doi: 10.1038/s44318-026-00712-4

Figure Lengend Snippet: ( A , B ) Transcriptomics data of single-cell suspensions from whole WT mouse lungs. The featured plot shows the average expression level of MMPs based on unique molecular identifier (UMI) counts (coded by color grading). MMP expression was determined in 32 different cell types. Shown are MMP2, 3, 7, 8, 9, 12, 13, 14, 19. ( C – N ) Quantification of the levels of different MMPs in macrophage (AMΦ and IMΦ) and pmLF supernatants (SN) isolated from WT and Trpml1 −/− mice using ELISA. IMΦ/pmLF SN: One single dot corresponds to one biologically independent sample, i.e., one mouse. AMΦ SN: One single dot corresponds to one well. Six WT and six Trpml1 −/− mice were lavaged to obtain the appropriate number of cells for all wells. Statistical analysis of all datasets was performed using Student’s t -test, unpaired, two-tailed. * p < 0.05, *** p < 0.001. All data were mean ± SEM. Exact p values were: pmLF SN, MMP2, p = 0.0141; AM SN, MMP8, p = 0.0430; pmLF SN, MMP9, p = 0.0241; IM SN, MMP9, p = 0.0327; AM SN, MMP12, p = 0.0002; IM SN MMP12, p = 0.097; pmLF SN, MMP19, p = 0.0124. .

Article Snippet: The following ELISAs were used for the experiments: SP-A ELISA (NBP2-76693, Novus biologicals), Cathepsin K ELISA (NBP3-00426, Novus biologicals), TIMP1 ELISA (ab196265, Abcam), TIMP2 ELISA (ab227893, Abcam), MMP1 ELISA (NBP3-06885, Novus biologicals and ABIN6963621, Antibodies online), MMP2 ELISA (ab254516, Abcam), MMP3 ELISA (ab100731), MMP8 ELISA (ab206982, Abcam), MMP9 ELISA (MMPT90, R&D systems), MMP12 ELISA (ab213878, Abcam), MMP13 ELISA (NBP3-06930, Novus biologicals), MMP14 ELISA (NBP3-06941, Novus biologicals and ABIN6957687, Antibodies online), MMP19 ELISA (NBP3-06941, Novus biologicals), IL-17A ELISA (ab199081, Abcam), DESMOSINE ELISA (CSB-E14196m, Cusabio).

Techniques: Transcriptomics, Single Cell, Expressing, Isolation, Enzyme-linked Immunosorbent Assay, Two Tailed Test

Journal: The EMBO Journal

Article Title: TRPML1 suppresses pulmonary fibrosis by limiting collagen and elastin deposition

doi: 10.1038/s44318-026-00712-4

Figure Lengend Snippet: ( A ) UMAP plot showing annotated cell clusters. Major cell types are labeled and color-coded, including epithelial, immune, endothelial, and stromal populations. MMP expression was determined in 32 different cell types. ( B ) UMAP plots showing the expression of selected MMP genes (MMP10, 11, 15, 16, 17, 20, 21, 23, 24, 25, 27, 28) in single cells from mouse lung tissue (filtered air group, n = 9). Expression is color-coded by log-normalized expression levels, with darker shades indicating higher expression. ( C – E ) qRT-PCR data showing mRNA expression levels of Mmp1a, Mmp1b, Mmp2, Mmp3, Mmp9, Mmp12, Mmp13, Mmp14, and Mmp19 in pmLF, IMΦ or AMΦ (WT and Trpml1 −/− ). ( F ) qRT-PCR data showing mRNA expression levels of Timp1, Timp2, Timp3, Timp4 in pmLF and IMΦ (WT and Trpml1 −/− ). In all figures, each single dot corresponds to one biologically independent sample. Data were mean ± SEM. Statistical analysis for qRT-PCR data were performed with multiple t -test, corrected for multiple comparisons using the Holm–Šídák method. ( G – J ) Western Blot analysis of different MMPs in pmLF isolated from WT and Trpml1 −/− mice. Graphs show quantification of each MMP band normalized to ß-actin. Each single dot corresponds to cells isolated from one mouse. Data were mean ± SEM. Student’s t -test, unpaired, two-tailed. .

Article Snippet: The following ELISAs were used for the experiments: SP-A ELISA (NBP2-76693, Novus biologicals), Cathepsin K ELISA (NBP3-00426, Novus biologicals), TIMP1 ELISA (ab196265, Abcam), TIMP2 ELISA (ab227893, Abcam), MMP1 ELISA (NBP3-06885, Novus biologicals and ABIN6963621, Antibodies online), MMP2 ELISA (ab254516, Abcam), MMP3 ELISA (ab100731), MMP8 ELISA (ab206982, Abcam), MMP9 ELISA (MMPT90, R&D systems), MMP12 ELISA (ab213878, Abcam), MMP13 ELISA (NBP3-06930, Novus biologicals), MMP14 ELISA (NBP3-06941, Novus biologicals and ABIN6957687, Antibodies online), MMP19 ELISA (NBP3-06941, Novus biologicals), IL-17A ELISA (ab199081, Abcam), DESMOSINE ELISA (CSB-E14196m, Cusabio).

Techniques: Labeling, Expressing, Quantitative RT-PCR, Western Blot, Isolation, Two Tailed Test

Journal: The EMBO Journal

Article Title: TRPML1 suppresses pulmonary fibrosis by limiting collagen and elastin deposition

doi: 10.1038/s44318-026-00712-4

Figure Lengend Snippet: ( A ) Knockdown efficiency of the targeted gene determined by qPCR, shown as fold change relative to the non-targeting (NT) control and normalized to the housekeeping gene ( n = 4–6 biological replicates). Data were mean ± SEM. Statistical significance was determined using two-way ANOVA followed by Holm–Šídák’s multiple comparisons test. Shown are mean values ± SEM. ** p < 0.01, **** p < 0.0001. Exact p values were: GAPDH, p < 0.0001; MMP2, p = 0.0154; MMP9, p < 0.0001; MMP19, p = 0.0016. ( B ) Zymography-based MMP activity measured as absolute final fluorescence values, representing the total collagen degraded in each sample at reaction endpoint ( n = 4–6 biological replicates). Data were mean ± SEM. Statistical significance was determined using a paired t -test, comparing non-targeting control and MMP knockdown from the same mouse. Statistical significance was defined as * p < 0.05 and ** p < 0.01. Exact p values were: MMP2, p = 0.0017; MMP9, p = 0.0059; MMP19, p = 0.0413. ( C ) Shown are the chemical structures of TRPML1 compounds used in this study, provided by Casma Therapeutics. .

Article Snippet: The following ELISAs were used for the experiments: SP-A ELISA (NBP2-76693, Novus biologicals), Cathepsin K ELISA (NBP3-00426, Novus biologicals), TIMP1 ELISA (ab196265, Abcam), TIMP2 ELISA (ab227893, Abcam), MMP1 ELISA (NBP3-06885, Novus biologicals and ABIN6963621, Antibodies online), MMP2 ELISA (ab254516, Abcam), MMP3 ELISA (ab100731), MMP8 ELISA (ab206982, Abcam), MMP9 ELISA (MMPT90, R&D systems), MMP12 ELISA (ab213878, Abcam), MMP13 ELISA (NBP3-06930, Novus biologicals), MMP14 ELISA (NBP3-06941, Novus biologicals and ABIN6957687, Antibodies online), MMP19 ELISA (NBP3-06941, Novus biologicals), IL-17A ELISA (ab199081, Abcam), DESMOSINE ELISA (CSB-E14196m, Cusabio).

Techniques: Knockdown, Control, Zymography, Activity Assay, Fluorescence

Journal: The EMBO Journal

Article Title: TRPML1 suppresses pulmonary fibrosis by limiting collagen and elastin deposition

doi: 10.1038/s44318-026-00712-4

Figure Lengend Snippet: ( A ) Quantification of the levels of MMP2, 9, 19 in pmLF SN and MMP12 in AMΦ SN isolated from 3.5-month-old WT and Trpml1 −/− mice using ELISA after pretreatment with the TRPML1 agonist WR1-002 (C8). One single dot corresponds to one well. 7 WT and Trpml1 −/− mice were lavaged to obtain the appropriate number of cells for all wells. Statistical analysis of all datasets was performed using Student’s t -test, unpaired, two-tailed. ** p < 0.01. All data were mean ± SEM. Values were normalized to DMSO-treated WT controls. Exact p values were as follows: comparison of WT SN to WT SN treated with WR1-002 (C8) 5 µM - pmLF SN, MMP2, p = 0.0459; pmLF SN, MMP9, p = 0.0371; pmLF SN, MMP19, p < 0.0001; AM SN, MMP12, p = 0.0043. ( B – D ) Cartoons illustrating fibroblasts, macrophages and other cell types in the lung ( B , C ) as well as the trafficking and secretion dynamics of MMPs and TIMPs in WT, Trpml1 −/− , and Trpml3 −/− lung macrophages ( D ). In WT macrophages, MMPs and TIMPs are trafficking through the trans-Golgi network (TGN) and are being secreted either directly from the TGN or via lysosomes (LY). In Trpml1 −/− macrophages, lysosomal exocytosis of such latter MMPs is impaired, leading to reduced MMP levels in the extracellular space. Endocytosis and intracellular trafficking remain intact, and secretion of MMPs directly from the TGN is unaffected. This disruption results in a restrictive lung phenotype. Conversely, Trpml3 −/− macrophages show impaired endocytosis and intracellular trafficking, but lysosomal exocytosis is preserved. This leads to the accumulation of ELS (endolysosomal system) dependent MMPs in the extracellular space, contributing to an obstructive lung phenotype. Trpml1 −/− and Trpml3 −/− show contrasting roles in regulating ELS-dependent MMP secretion and their opposing effects on lung pathology. .

Article Snippet: The following ELISAs were used for the experiments: SP-A ELISA (NBP2-76693, Novus biologicals), Cathepsin K ELISA (NBP3-00426, Novus biologicals), TIMP1 ELISA (ab196265, Abcam), TIMP2 ELISA (ab227893, Abcam), MMP1 ELISA (NBP3-06885, Novus biologicals and ABIN6963621, Antibodies online), MMP2 ELISA (ab254516, Abcam), MMP3 ELISA (ab100731), MMP8 ELISA (ab206982, Abcam), MMP9 ELISA (MMPT90, R&D systems), MMP12 ELISA (ab213878, Abcam), MMP13 ELISA (NBP3-06930, Novus biologicals), MMP14 ELISA (NBP3-06941, Novus biologicals and ABIN6957687, Antibodies online), MMP19 ELISA (NBP3-06941, Novus biologicals), IL-17A ELISA (ab199081, Abcam), DESMOSINE ELISA (CSB-E14196m, Cusabio).

Techniques: Isolation, Enzyme-linked Immunosorbent Assay, Two Tailed Test, Comparison, Disruption