Journal: Pathophysiology

Article Title: Bioinformatic Analysis of Contrasting Expression Patterns and Molecular Interactions of TIMPs in Breast Cancer: Implications for Tumor Progression and Survival

doi: 10.3390/pathophysiology33010013

Figure Lengend Snippet: Expression levels of TIMPs across breast cancer molecular subtypes. Violin plots showing the relative expression (Z-score) of TIMP genes across breast cancer molecular subtypes: Luminal A ( n = 499), Luminal B ( n = 197), HER2+ ( n = 78), basal (TN) ( n = 171), and normal-like ( n = 36). ( A ) TIMP1 gene expression. ( B ) TIMP2 gene expression. ( C ) TIMP3 gene expression. ( D ) TIMP4 gene expression. Data were obtained from the TCGA PanCancer Breast Invasive Carcinoma dataset via cBioPortal for Cancer Genomics. Gene expression values are represented as Z-scores relative to normal tissue samples. Statistical analyses were performed using one-way ANOVA, followed by Bonferroni post hoc tests to compare gene expression levels across molecular subtypes relative to the Luminal A subtype. Statistical significance relative to Luminal A samples is indicated as p < 0.05 (*), p < 0.01 (**), p < 0.001 (***), and p < 0.0001 (****).

Article Snippet: It is important to note that, to date, the Human Protein Atlas includes no data reporting the protein expression of TIMP3 and TIMP4.

Techniques: Expressing, Gene Expression

Journal: Pathophysiology

Article Title: Bioinformatic Analysis of Contrasting Expression Patterns and Molecular Interactions of TIMPs in Breast Cancer: Implications for Tumor Progression and Survival

doi: 10.3390/pathophysiology33010013

Figure Lengend Snippet: Expression levels of TIMPs across breast cancer tumor stages. Analysis of TIMP1 ( A ), TIMP2 ( B ), TIMP3 ( C ), and TIMP4 ( D ) gene expression in breast tumor samples classified by tumor stage from I to IV. Values are expressed as Z-scores relative to normal tissue samples. Violin plots show the distribution and density of the data within each group. Statistical analyses were performed using one-way ANOVA followed by Bonferroni post hoc tests to compare expression levels across tumor stages relative to stage I. Statistical significance relative to stage I is indicated as p < 0.05 (*) and p < 0.01 (**).

Article Snippet: It is important to note that, to date, the Human Protein Atlas includes no data reporting the protein expression of TIMP3 and TIMP4.

Techniques: Expressing, Gene Expression

Journal: Pathophysiology

Article Title: Bioinformatic Analysis of Contrasting Expression Patterns and Molecular Interactions of TIMPs in Breast Cancer: Implications for Tumor Progression and Survival

doi: 10.3390/pathophysiology33010013

Figure Lengend Snippet: TIMP expression levels in different molecular subtypes of breast cancer patient samples and cell lines. Gene expression analysis of TIMP1 ( A ), TIMP2 ( B ), TIMP3 ( C ), and TIMP4 ( D ). Dataset GSE45827 shows the corresponding TIMP expression in different molecular subtypes of breast tumor samples. Dataset GSE4813 shows TIMP expression in cell lines classified into different molecular subtypes of breast cancer. Statistical analyses were performed using one-way ANOVA followed by Dunnett’s tests to compare expression levels across tumor stages. Statistical significance is indicated as p < 0.05 (*), p < 0.001 (***). The frequency of breast cancer and normal samples showing TIMP1 and TIMP2 protein expression, negative (N), low (L), medium (M), and high (H), are represented in sections ( E , F ). Sections ( G , H ) show representative images of TIMP1 and TIMP2 in breast cancer and normal samples, respectively.

Article Snippet: It is important to note that, to date, the Human Protein Atlas includes no data reporting the protein expression of TIMP3 and TIMP4.

Techniques: Expressing, Gene Expression

Journal: Pathophysiology

Article Title: Bioinformatic Analysis of Contrasting Expression Patterns and Molecular Interactions of TIMPs in Breast Cancer: Implications for Tumor Progression and Survival

doi: 10.3390/pathophysiology33010013

Figure Lengend Snippet: Expression levels of TIMPs and their correlation with overall survival (OS) in breast cancer patients. Red lines represent low TIMP expression, and blue lines represent high TIMP expression. The Y-axis represents the probability of survival, and the X-axis represents patient follow-up time. A representative p -value is shown in each graph. Univariate Cox regression models were applied to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). ( A ) Correlation between TIMP1 expression and OS; ( B ) correlation between TIMP2 expression and OS; ( C ) correlation between TIMP3 expression and OS; and ( D ) correlation between TIMP4 expression and OS.

Article Snippet: It is important to note that, to date, the Human Protein Atlas includes no data reporting the protein expression of TIMP3 and TIMP4.

Techniques: Expressing

Journal: Pathophysiology

Article Title: Bioinformatic Analysis of Contrasting Expression Patterns and Molecular Interactions of TIMPs in Breast Cancer: Implications for Tumor Progression and Survival

doi: 10.3390/pathophysiology33010013

Figure Lengend Snippet: Positive correlation of TIMP3 with KEGG signaling pathways and GO enrichment in breast cancer. KEGG and GO analysis ( https://bio.tools/david_bioinformatics_resources , accessed on 11 November 2025). Categorization into Biological Processes (BPs), Cellular Components (CCs), Molecular Functions (MFs), and Kyoto Encyclopedia of Genes and Genomes (KEGG). Data were organized and are presented as bubble plots. Only data with statistical significance ( p < 0.05) were included.

Article Snippet: It is important to note that, to date, the Human Protein Atlas includes no data reporting the protein expression of TIMP3 and TIMP4.

Techniques: Protein-Protein interactions

Journal: Pathophysiology

Article Title: Bioinformatic Analysis of Contrasting Expression Patterns and Molecular Interactions of TIMPs in Breast Cancer: Implications for Tumor Progression and Survival

doi: 10.3390/pathophysiology33010013

Figure Lengend Snippet: Association between TIMP expression and immune cell infiltration in breast cancer. ( A ) Heatmap showing Spearman correlation coefficients between the expression levels of TIMP1 , TIMP2 , TIMP3 , and TIMP4 and the estimated infiltration fractions of major immune and stromal cell populations, as inferred by the EPIC algorithm using the TCGA PanCancer Breast Invasive Carcinoma dataset via cBioPortal for Cancer Genomics RNA-seq data. Color intensity represents the direction and magnitude of the correlation (red, positive; blue, negative). Statistical significance is indicated as p < 0.01 (**) and p < 0.001 (***). ( B – E ) Violin plots comparing immune and stromal cell infiltration levels between high- and low-expression groups for TIMP1 ( B ), TIMP2 ( C ), TIMP3 ( D ), |and TIMP4 ( E ). Patients were stratified based on the median expression value of each TIMP. Estimated cell fractions are shown for B cells, CAFs, CD4 + T cells, CD8 + T cells, endothelial cells, macrophages, NK cells, and other cells. Statistical differences between groups were assessed using the Wilcoxon rank-sum test with Benjamini–Hochberg false discovery rate correction. Significance levels are indicated as p < 0.01 (**), p < 0.001 (***), and p < 0.0001 (****).

Article Snippet: It is important to note that, to date, the Human Protein Atlas includes no data reporting the protein expression of TIMP3 and TIMP4.

Techniques: Expressing, RNA Sequencing

Journal: Clinical Ophthalmology (Auckland, N.Z.)

Article Title: Sorsby Fundus Dystrophy in an Asian Pedigree: Pathogenic Timp3 P.Y191c Variant Impairs Its Binding with Mmp2/9 and Cellular Localization

doi: 10.2147/OPTH.S556592

Figure Lengend Snippet: Whole exome sequencing. ( A ) Sanger sequencing chromatograms of twelve family members identified the heterozygous c.572A>G (p. Y191C ) TIMP3 variant in the proband (III:5), his father (II:6), uncle (II:3, II:8), aunt (II:11), and cousins (III:3, III:10). ( B ) Pedigree analysis illustrating the inheritance of the c.572A>G (p. Y191C ) variant. ( C ) Multiple sequence alignments of TIMP3 Tyr191 across species revealed that the variant occurred in highly conserved residues. ( D ) Schematic structures of the original and mutant amino acids, highlighting the backbone in red and the side chain in black. ( E ) Comparative 3D structures of the wild-type ( a ) and mutant ( b ) proteins.

Article Snippet: Primary antibodies included TIMP3 (Proteintech, 10858-1-AP, WB: 1:2000, IP: 1:1000, IF: 1:400), MMP9 (Proteintech, 10375-2-AP, WB: 1:600, IP:1:500, IF: 1:100), MMP2 (Proteintech, 66366-1-Ig, WB: 1:1000, IP:1:500, IF: 1:200), and GAPDH (Abcam, ab8245, 1:5000).

Techniques: Sequencing, Variant Assay, Mutagenesis

Journal: Clinical Ophthalmology (Auckland, N.Z.)

Article Title: Sorsby Fundus Dystrophy in an Asian Pedigree: Pathogenic Timp3 P.Y191c Variant Impairs Its Binding with Mmp2/9 and Cellular Localization

doi: 10.2147/OPTH.S556592

Figure Lengend Snippet: The TIMP3 variant Y191C mitigated the cell viability and promoted the apoptosis of ARPE-19. ( A ) CCK-8 assay demonstrated a significant reduction in cell viability in the MT group compared to the empty vector control group 24 hours post-LPS treatment ( P= 0.0096), while no significant difference was observed in the WT group ( P= 0.7128). ( B and C ) Flow cytometry analysis indicated a significant increase in apoptosis rates in the MT group compared to the empty vector control group following LPS treatment ( P= 0.0005). In contrast, the WT group exhibited a 10% reduction in apoptosis rates compared to the empty vector control group. FIGURE 4 The TIMP3 variant Y191C mitigated the cell viability and promoted the apoptosis of ARPE-19. ( A ) CCK-8 assay demonstrated a significant reduction in cell viability in the MT group compared to the empty vector control group 24 hours post-LPS treatment ( P= 0.0096), while no significant difference was observed in the WT group ( P= 0.7128). ( B and C ) Flow cytometry analysis indicated a significant increase in apoptosis rates in the MT group compared to the empty vector control group following LPS treatment ( P= 0.0005). In contrast, the WT group exhibited a 10% reduction in apoptosis rates compared to the empty vector control group. n=3/group. “n” denotes biological replicates, defined as independently assayed aliquots derived from the same lentiviral infection and differentiation batch.

Article Snippet: Primary antibodies included TIMP3 (Proteintech, 10858-1-AP, WB: 1:2000, IP: 1:1000, IF: 1:400), MMP9 (Proteintech, 10375-2-AP, WB: 1:600, IP:1:500, IF: 1:100), MMP2 (Proteintech, 66366-1-Ig, WB: 1:1000, IP:1:500, IF: 1:200), and GAPDH (Abcam, ab8245, 1:5000).

Techniques: Variant Assay, CCK-8 Assay, Plasmid Preparation, Control, Flow Cytometry, Derivative Assay, Infection

Journal: Clinical Ophthalmology (Auckland, N.Z.)

Article Title: Sorsby Fundus Dystrophy in an Asian Pedigree: Pathogenic Timp3 P.Y191c Variant Impairs Its Binding with Mmp2/9 and Cellular Localization

doi: 10.2147/OPTH.S556592

Figure Lengend Snippet: The Y191C variant inhibited the interaction between TIMP3 and MMP proteins. ( A and B ) The Y191C mutation increases FLAG-TIMP3 complex formation, selectively enhancing interaction with MMP9 proteolytic fragments (45~55 kDa) while reducing MMP2 binding. ( C – E ) Following LPS administration, MMP2 expression levels in the empty vector control group remained comparable to those in the normal control group. However, in the MT group, MMP2 expression was significantly elevated compared to the empty vector group ( P < 0.0001, 1.84 ± 0.21-fold) and showed a modest increase compared to the WT control group ( P= 0.0889, 1.15 ± 0.13-fold). Additionally, MMP9 expression in the MT group was markedly higher than in the empty vector group after LPS treatment ( P < 0.0172, 2.12 ± 0.41-fold). ( F ) IF staining revealed nuclear localization of MMP2 in ARPE-19 cells of the WT group, whereas in the MT group, MMP2 expression extended into the cytoplasm of ARPE-19 cells. n=3/group. “n” refers to the number of independent biological replicates.

Article Snippet: Primary antibodies included TIMP3 (Proteintech, 10858-1-AP, WB: 1:2000, IP: 1:1000, IF: 1:400), MMP9 (Proteintech, 10375-2-AP, WB: 1:600, IP:1:500, IF: 1:100), MMP2 (Proteintech, 66366-1-Ig, WB: 1:1000, IP:1:500, IF: 1:200), and GAPDH (Abcam, ab8245, 1:5000).

Techniques: Variant Assay, Mutagenesis, Binding Assay, Expressing, Plasmid Preparation, Control, Staining

Journal: Cell Death & Disease

Article Title: Genetic removal of Nlrp3 protects against age-related and R345W Efemp1-induced basal laminar deposit formation

doi: 10.1038/s41419-025-08104-y

Figure Lengend Snippet: A mRNA was extracted from WT or R345W +/+ RPE/choroid samples, reverse transcribed and probed for transcript levels of complement component 3 (C3, p ≤ 0.05), caspase 1 (Casp1), interleukin 18 (Il18), interleukin 1 beta (Il1β), interleukin 6 (Il6), nucleotide-binding oligomerization (NOD)-like receptor protein 3 (Nlrp3), complement factor H (Cfh), Efemp1 (FBLN3, F3), tissue inhibitor of matrix metalloproteinase 3 (Timp3) and plotted relative to β-actin ( n = 5–6 mice). 2-way ANOVA. Mean ± S.D. * p < 0.05.

Article Snippet: Available TaqMan probes (Applied Biosystems, Waltham, MA) were used for qPCR reactions as follows: β-actin (Mm02619580_g1), C3 (Mm01232779_m1), Casp1 (mm00438023_m1), Cfh (Mm01299248_m1), Efemp1 (Mm00524588_m1), Gfap (Mm01253033_m1), Il18 (mm00434226_m1), Il1β (Mm00434228_m1), Il6 (Mm00446190_m1), Nlrp3 (mm00840904_m1), and Timp3 (Mm00441826_m1).

Techniques: Reverse Transcription, Binding Assay