Journal: Physiological Reports

Article Title: Elimination of hepatocyte‐derived DPP4 downregulates cardiac immune‐ and collagen‐related genes but does not alter cardiac function in aged male mice

doi: 10.14814/phy2.70453

Figure Lengend Snippet: Fibrosis‐related genes are upregulated in Dpp4 −/− mice and unchanged in Dpp4 hep−/− mice, but no differences were detected in senescence and metabolism‐related genes. Ventricular mRNA abundance (relative to Gapdh ) of hypertrophic and ECM modeling‐related genes (a) Col1a1 , (b) Col3a1 , (c) Ctgf , (d) Myh7 , (e) Nppa , (f) Nppb , (g) Mmp2 , (h) Mmp9 , (i) Ddr2 , and (j) Vim . Senescence and cell cycle genes (k) Ankrd1 and (l) Cdkn1a . Metabolism‐related genes (m) Pnpla2 , (n) Acadm , (o) Cd36 , (p) Pgc1α , (q) Dgat1 , (r) Pdk4 , (s) Cpt1b , and (t) Slc27a1 . Data are presented as the means ± SEM, analyzed by unpaired students t ‐test with Welch's correction, ns p < 0.05.

Article Snippet: Discoidin domain receptor family, member 2 ( Ddr2 ) , Mm00445614_m1.

Techniques:

Journal: bioRxiv

Article Title: Loss of the Y chromosome in bladder cancer drives metabolic reprogramming

doi: 10.1101/2025.08.26.672471

Figure Lengend Snippet: (A) TCGA cohort analysis of gene expressions; DDR2 expression is higher in male BC patients with low Y chromosome gene expression. (B and C) DDR2 protein expression is higher in YnegN cell cytoplasm and nuclei. (D) Heatmap of 50 metabolites with highest fold differences in DMA of DDR2KO_YnegN vs CON_YnegN cells. (E) Volcano plot analysis for significant metabolites. with p-value cut off at 0.1 and fold difference cut off at 1.2. (F and G) Metabolic Pathways enrichment analysis (F) and MESA (G). (H) Integrated pathways analysis of DMA and DEG in DDR2KO_YnegN vs CON_YnegN cells. (I) Dot plot summarizes average glycolytic scores and the proportion of cells, indicating glycolysis-related genes expression across experimental groups; DDR2_Negative and DDR2_Positive). Dot size corresponds to the fraction of cells in each group expressing the pathway, and color intensity reflects the mean module score. Color scale ranges from −0.4 to +0.4. (J and K) Relative Glucose (J) and Lactate (K) abundances in CON_YnegN and DDR2KO_YnegN cells. (L) Normalized gene expression analysis from total-RNAseq data of both CON_YnegN and DDR2KO_YnegN cells, genes belong to the KEGG metabolism genes, proliferation genes, cell cycle genes, and Hallmark geneset of cancer stemness, EMT, and immune evasion genes. (M and N) Quantification of nuclei positive for Click_IT-Edu cell proliferation (M) and Ki67 proliferation/division assay (N). (O) Cell surface expression of cancer stem cell marker CD133 by flow cytometry analysis. (P) SNAIL1 ; EMT gene expression analysis by qPCR (Q) Surface expression of MHC-I on CON_YnegN and DDR2KO_YnegN cells analyzed by flow cytometry. Significance was calculated using either pairwise comparison (t-test) with welch correction (K, M-Q) or with 2-way ANOVA with multiple comparisons (J): *p < 0.05, **p < 0.01, and ****p < 0.0001.

Article Snippet: The primary antibody for DDR2 (Proteintech, 67126-1-Ig) was incubated overnight at 4°C and then washed three times with PBS for 10 minutes each time.

Techniques: Expressing, Gene Expression, Marker, Flow Cytometry, Comparison

Journal: bioRxiv

Article Title: Loss of the Y chromosome in bladder cancer drives metabolic reprogramming

doi: 10.1101/2025.08.26.672471

Figure Lengend Snippet: (A) HIF-1a gene expression analysis by qPCR. (B) Cell cycle analysis of CON_YnegN and DDR2KO_YNEGN cells; stage specific cell percentage quantitation. (C) MTS cell viability assay of CON_YnegN and DDR2KO_YNEGN cells, relative absorbance is plotted up to 72h. (D) Quantitation of cell percentages in specific apoptotic stage of for CON_YnegN and DDR2KO_YnegN cells from AnnexinV/PI apoptosis assay. (E) Immunoblot analysis of apoptotic pathway specific protein and phosphoproteins. (F) Immunofluorescence images of YposN and YnegN cells with DDR2. (G) Ven diagram showing the differential DDR2 interactomes in YposN and YnegN cells. (H) Metascape gene list analysis report for processes and pathways that includes the DDR2 interactomes found in YposN and YnegN cells. (I and K) Immunoblot analysis of spatial distribution of DDR and metabolic enzymes in cytoplasm and nucleus of YposN and YnegN cells, and quantitation (K). (J and L) Immunoblot analysis of spatial distribution of DDR2 and metabolic enzymes in cytoplasm and nucleus of CON_YnegN and DDR2KO_YnegN cells, and quantitation (L). Scale bars: 20 mM (F). Significance was calculated using either pairwise comparison (t-test) with welch correction (A, C) or with 2-way ANOVA with multiple comparisons (D, K, L): *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.

Article Snippet: The primary antibody for DDR2 (Proteintech, 67126-1-Ig) was incubated overnight at 4°C and then washed three times with PBS for 10 minutes each time.

Techniques: Gene Expression, Cell Cycle Assay, Quantitation Assay, Viability Assay, Apoptosis Assay, Western Blot, Immunofluorescence, Comparison

Journal: bioRxiv

Article Title: Loss of the Y chromosome in bladder cancer drives metabolic reprogramming

doi: 10.1101/2025.08.26.672471

Figure Lengend Snippet: (A) TCGA cohort analysis of gene expressions; DDR2 expression is higher in male BC patients with low Y chromosome gene expression. (B and C) DDR2 protein expression is higher in YnegN cell cytoplasm and nuclei. (D) Heatmap of 50 metabolites with highest fold differences in DMA of DDR2KO_YnegN vs CON_YnegN cells. (E) Volcano plot analysis for significant metabolites. with p-value cut off at 0.1 and fold difference cut off at 1.2. (F and G) Metabolic Pathways enrichment analysis (F) and MESA (G). (H) Integrated pathways analysis of DMA and DEG in DDR2KO_YnegN vs CON_YnegN cells. (I) Dot plot summarizes average glycolytic scores and the proportion of cells, indicating glycolysis-related genes expression across experimental groups; DDR2_Negative and DDR2_Positive). Dot size corresponds to the fraction of cells in each group expressing the pathway, and color intensity reflects the mean module score. Color scale ranges from −0.4 to +0.4. (J and K) Relative Glucose (J) and Lactate (K) abundances in CON_YnegN and DDR2KO_YnegN cells. (L) Normalized gene expression analysis from total-RNAseq data of both CON_YnegN and DDR2KO_YnegN cells, genes belong to the KEGG metabolism genes, proliferation genes, cell cycle genes, and Hallmark geneset of cancer stemness, EMT, and immune evasion genes. (M and N) Quantification of nuclei positive for Click_IT-Edu cell proliferation (M) and Ki67 proliferation/division assay (N). (O) Cell surface expression of cancer stem cell marker CD133 by flow cytometry analysis. (P) SNAIL1 ; EMT gene expression analysis by qPCR (Q) Surface expression of MHC-I on CON_YnegN and DDR2KO_YnegN cells analyzed by flow cytometry. Significance was calculated using either pairwise comparison (t-test) with welch correction (K, M-Q) or with 2-way ANOVA with multiple comparisons (J): *p < 0.05, **p < 0.01, and ****p < 0.0001.

Article Snippet: The protein lysates were incubated with mouse IgG monoclonal DDR2 antibody (Proteintech, 67126-1-Ig) at 4°C overnight with gentle mixing end over end shaker.

Techniques: Expressing, Gene Expression, Marker, Flow Cytometry, Comparison

Journal: bioRxiv

Article Title: Loss of the Y chromosome in bladder cancer drives metabolic reprogramming

doi: 10.1101/2025.08.26.672471

Figure Lengend Snippet: (A) HIF-1a gene expression analysis by qPCR. (B) Cell cycle analysis of CON_YnegN and DDR2KO_YNEGN cells; stage specific cell percentage quantitation. (C) MTS cell viability assay of CON_YnegN and DDR2KO_YNEGN cells, relative absorbance is plotted up to 72h. (D) Quantitation of cell percentages in specific apoptotic stage of for CON_YnegN and DDR2KO_YnegN cells from AnnexinV/PI apoptosis assay. (E) Immunoblot analysis of apoptotic pathway specific protein and phosphoproteins. (F) Immunofluorescence images of YposN and YnegN cells with DDR2. (G) Ven diagram showing the differential DDR2 interactomes in YposN and YnegN cells. (H) Metascape gene list analysis report for processes and pathways that includes the DDR2 interactomes found in YposN and YnegN cells. (I and K) Immunoblot analysis of spatial distribution of DDR and metabolic enzymes in cytoplasm and nucleus of YposN and YnegN cells, and quantitation (K). (J and L) Immunoblot analysis of spatial distribution of DDR2 and metabolic enzymes in cytoplasm and nucleus of CON_YnegN and DDR2KO_YnegN cells, and quantitation (L). Scale bars: 20 mM (F). Significance was calculated using either pairwise comparison (t-test) with welch correction (A, C) or with 2-way ANOVA with multiple comparisons (D, K, L): *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.

Article Snippet: The protein lysates were incubated with mouse IgG monoclonal DDR2 antibody (Proteintech, 67126-1-Ig) at 4°C overnight with gentle mixing end over end shaker.

Techniques: Gene Expression, Cell Cycle Assay, Quantitation Assay, Viability Assay, Apoptosis Assay, Western Blot, Immunofluorescence, Comparison