Journal: Molecular Therapy Oncology

Article Title: Collagen depletion by pirfenidone enhances antitumor effect of oncolytic adenovirus against peritoneal metastases of gastric cancer

doi: 10.1016/j.omton.2025.201045

Figure Lengend Snippet: GC cells increase collagen 1 expression in fibroblasts and collagen increases proliferation of GC cells (A) Expressions of Col1A1, Col1A2, and ACTA2 mRNA in mouse gastric cancer (GC) cells (T3-2D), human GC cells (MKN45, MKN7, and NUGC4), mouse fibroblast cells (MEF), and human fibroblast cells (YS-1 and FEF3) are shown. All cells were analyzed by quantitative RT-PCR analysis. Data are expressed as the mean ± SD ( n = 3). (B) Expression of Col1A1 and Col1A2 mRNA in MEF (upper) and YS-1 (lower) cells after incubation with serum-free medium (SFM) as a control and conditioned medium (CM) of each GC cell type for 4 days. Cells were analyzed using quantitative RT-PCR analysis. Data are expressed as the mean ± SD ( n = 3). (C) Representative images of immunocytochemical staining of collagen 1 and α-SMA in MEF (left) and YS-1 (right) after incubation with normal medium and CM of each of the GC cells for 4 days. SFM was used as a control. The area index for each staining was evaluated by ImageJ software. Data are expressed as the mean ± SD ( n = 3). Scale bars, 50 μm. (D) Cell proliferation of T3-2D and MKN45 cells with and without 10% collagen stimulation for 72 h. Data are expressed as the mean ± SD ( n = 5). (E) Representative cellular morphological images of T3-2D and MKN45 cells with and without 10% collagen 1 stimulation for 72 h. Scale bar, 100 μm. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ∗∗∗∗ p < 0.0001.

Article Snippet: Primary antibodies against rabbit anti-Col1A1 mAb (E8F4L, 1:200; Cell Signaling Technology), rabbit anti-α-SMA mAb (19245, 1:500; Cell Signaling Technology), mouse anti-CD8a mAb (4SM15, 1:200; eBioscience, San Diego, CA), rabbit anti-CD163 mAb (ab182422, 1:500; Abcam), and rabbit anti-adenovirus type VpAb (ab6982, 1:800; Abcam) were used.

Techniques: Expressing, Quantitative RT-PCR, Incubation, Control, Staining, Software

Journal: Molecular Therapy Oncology

Article Title: Collagen depletion by pirfenidone enhances antitumor effect of oncolytic adenovirus against peritoneal metastases of gastric cancer

doi: 10.1016/j.omton.2025.201045

Figure Lengend Snippet: Antitumor effect of OBP-702 was attenuated in collagen-rich PM of GC T3-2D (5 ×10 4 cells) cells alone and those co-inoculated with MEF (5 ×10 5 cells) were inoculated into the abdominal cavity of C57BL/6J mice and treated with intraperitoneal administration of PBS or OBP-702 (1 × 10 8 PFU/body) four times. (A) Schema of the treatment schedule. Red arrowheads show the timing of treatment with OBP-702 and the black cross indicates sacrifice. (B) Body weight changes in mice of each group. (C) Macroscopic images of peritoneal nodules in each group. (D) The total number and weight of PMs were measured 17 days after tumor inoculation. Data are shown as the mean value ±SD ( n = 4). (E) Representative microscopic images with H&E, Masson trichrome, Col1A1, and α-SMA staining of peritoneal nodules in each group. Scale bars, 100 μm. (F) Area indexes of stroma, Col1A1, and α-SMA in each staining was evaluated by ImageJ software. The mean area index was calculated from three selected fields in each mouse, from a total of four mice per group. Data are expressed as the mean ± SD ( n = 4). ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ∗∗∗∗ p < 0.0001.

Article Snippet: Primary antibodies against rabbit anti-Col1A1 mAb (E8F4L, 1:200; Cell Signaling Technology), rabbit anti-α-SMA mAb (19245, 1:500; Cell Signaling Technology), mouse anti-CD8a mAb (4SM15, 1:200; eBioscience, San Diego, CA), rabbit anti-CD163 mAb (ab182422, 1:500; Abcam), and rabbit anti-adenovirus type VpAb (ab6982, 1:800; Abcam) were used.

Techniques: Staining, Software

Journal: Molecular Therapy Oncology

Article Title: Collagen depletion by pirfenidone enhances antitumor effect of oncolytic adenovirus against peritoneal metastases of gastric cancer

doi: 10.1016/j.omton.2025.201045

Figure Lengend Snippet: Pirfenidone (PFD) decreased collagen expression in CAFs and enhanced the antitumor effect of OBP-702 on spheroid models (A) The concentration of TGF-β in the CM of each GC cell was analyzed using ELISA. SFM was used as a control. (B) Representative images of immunocytochemical staining of collagen 1 and α-SMA in MEF and YS-1 cells after incubation with recombinant TGF-β for 4 days. SFM was used as a control. The area index for each staining was evaluated by ImageJ software. Data are expressed as the mean ± SD ( n = 3). Scale bars, 100 μm. (C) Representative images of immunocytochemical staining of collagen 1 in MEF and YS-1 cells after incubation with CM of T3-2D or MKN45 cells treated with PFD (1 mM) or OBP-702 (20 MOI or 50 MOI) for 4 days. SFM was used as a control. The area index for each staining was evaluated by ImageJ software. Data are expressed as the mean ± SD ( n = 3). Scale bars, 100 μm. (D) Representative images of T3-2D spheroids co-cultured with MEF after incubation with PFD (1 mM), OBP-702 (20 MOI), or in combination, for 7 days. (E) ATP cell viability assay of T3-2D and MEF co-culture of spheroids after treated with PFD (1 mM), OBP-702 (20 MOI), or in combination, for 7 days. Data are expressed as the mean ± SD ( n = 5). (F) Representative microscopic images with H&E, Col1A1 and anti-adenovirus type V staining of co-culture spheroids treated with PFD (1 mM), OBP-702 (20MOI) or in combination, for 7 days. Scale bars, 100 μm. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ∗∗∗∗ p < 0.0001.

Article Snippet: Primary antibodies against rabbit anti-Col1A1 mAb (E8F4L, 1:200; Cell Signaling Technology), rabbit anti-α-SMA mAb (19245, 1:500; Cell Signaling Technology), mouse anti-CD8a mAb (4SM15, 1:200; eBioscience, San Diego, CA), rabbit anti-CD163 mAb (ab182422, 1:500; Abcam), and rabbit anti-adenovirus type VpAb (ab6982, 1:800; Abcam) were used.

Techniques: Expressing, Concentration Assay, Enzyme-linked Immunosorbent Assay, Control, Staining, Incubation, Recombinant, Software, Cell Culture, Viability Assay, Co-Culture Assay

Journal: Molecular Therapy Oncology

Article Title: Collagen depletion by pirfenidone enhances antitumor effect of oncolytic adenovirus against peritoneal metastases of gastric cancer

doi: 10.1016/j.omton.2025.201045

Figure Lengend Snippet: Collagen depletion by pirfenidone (PFD) enhances the antitumor effects of OBP-702 in peritoneal metastasis (A) Schema of the treatment schedule. Orthotopic mouse peritoneal metastasis model of T3-2D and MEF co-injection treated by intraperitoneal administration of PBS, PFD, OBP-702, or the combination of PFD and OBP-702. Green arrowheads show the timing of treatments with PBS or OBP-702, and red arrowheads show treatments with PFD. The black cross indicates sacrifice. (B) The total number and weight of PM were measured 17 days after tumor inoculation. Data are shown as the mean value ±SD ( n = 5). (C) Kaplan-Meier curves for overall survival in mice treated with each treatment. (D) Representative microscopic images with H&E, Masson trichrome, Col1A1, α-SMA, and anti-adenovirus type V staining of peritoneal nodules in each group. Scale bars, 100 μm. (E) Area indexes of stroma, Col1A1, α-SMA, and adenovirus type V in the tumors were evaluated by ImageJ software. The mean area index was calculated from three selected fields in each mouse, from a total of five mice per group. Data are expressed as the mean ± SD ( n = 5). ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ∗∗∗∗ p < 0.0001.

Article Snippet: Primary antibodies against rabbit anti-Col1A1 mAb (E8F4L, 1:200; Cell Signaling Technology), rabbit anti-α-SMA mAb (19245, 1:500; Cell Signaling Technology), mouse anti-CD8a mAb (4SM15, 1:200; eBioscience, San Diego, CA), rabbit anti-CD163 mAb (ab182422, 1:500; Abcam), and rabbit anti-adenovirus type VpAb (ab6982, 1:800; Abcam) were used.

Techniques: Injection, Staining, Software

Journal: European Journal of Medical Research

Article Title: MiRNA-29b accelerates the PDGF in exosomes and stimulates hepatic stellate cells to promote liver fibrosis in biliary atresia

doi: 10.1186/s40001-025-02731-z

Figure Lengend Snippet: Effects of miRNA-29b overexpression and inhibition in exosomes on the expression of DNMT3a, DNMT3b, PDGFA, COL1A1, and α-SMA in LX-2 cells and verification of miRNA-29b target genes by dual luciferase assays. a miRNA-29b-overexpressing exosomes were cocultured with LX-2 cells, and the expression levels of DNMT3a and DNMT3b in the Up group were significantly decreased. b The transcription level of PDGFA in the b Up group was significantly increased. c The expression levels of COL1A1 and α-SMA in the Up group were increased. d Exosomes with low miRNA-29b expression were cocultured with LX-2 cells, and the expression levels of DNMT3a and DNMT3b in the Down group were significantly increased. e The expression level of PDGFA in the Down group was decreased. f The expression of COL1A1 and α-SMA decreased in the Down group. g Double luciferase experiments proved that DNMT3a and DNMT3b were the target genes of miR-29b-3p. Note: Normal: untreated LX-2 cells in the blank control group; control: negative empty exosomes were cocultured with LX-2 cells. Down: exosomes with low miRNA-29b expression were cocultured with LX-2 cells; a–f : LX-2 cells cocultured with exosomes from 3 independent experiments (n = 3); g: Data from 4 biological replicates (n = 4). * indicates p < 0.05 compared with the control group

Article Snippet: The membrane was blocked with 5% skim milk and incubated with primary antibodies against DNMT3a, DNMT3b, PDGFA, COL1A1 and α-SMA (GeneTex, Abcam).

Techniques: Over Expression, Inhibition, Expressing, Luciferase, Control

Journal: European Journal of Medical Research

Article Title: MiRNA-29b accelerates the PDGF in exosomes and stimulates hepatic stellate cells to promote liver fibrosis in biliary atresia

doi: 10.1186/s40001-025-02731-z

Figure Lengend Snippet: Effect of 5-AZAC on LX-2 cells cocultured with miRNA-29b overexpression and inhibition exosomes. a The miRNA-29b overexpression exosome + 5Azac group showed decreased expression of DNMT3a and DNMT3b; b the miRNA-29b overexpression exosome + 5Azac group showed increased expression of PDGFA; c The expression of COL1A1 and α-SMA in the miRNA-29b overexpressed exosome + 5Azac group increased; d The expression levels of DNMT3a and DNMT3b in the miRNA-29b low-expression exosome + 5Azac group were decreased; e the miRNA-29b low expression exosome + 5Azac group showed increased expression of PDGFA; f The expression of COL1A1 and α-SMA increased in the miRNA-29b low-expression exosome + 5Azac group. Note : Normal: untreated LX-2 cells in the blank control group; control: negative empty exosomes were cocultured with LX-2 cells. Up + 5Azac: miRNA-29b-overexpressing exosomes + 5Azac were cocultured with LX-2 cells. Down + 5Azac: Exosomes with low expression of miRNA-29b + 5Azac were cocultured with LX-2 cells; a – f : Data from 3 independent experiments (n = 3). * indicates p < 0.05 compared with the control group

Article Snippet: The membrane was blocked with 5% skim milk and incubated with primary antibodies against DNMT3a, DNMT3b, PDGFA, COL1A1 and α-SMA (GeneTex, Abcam).

Techniques: Over Expression, Inhibition, Expressing, Control

Journal: European Journal of Medical Research

Article Title: MiRNA-29b accelerates the PDGF in exosomes and stimulates hepatic stellate cells to promote liver fibrosis in biliary atresia

doi: 10.1186/s40001-025-02731-z

Figure Lengend Snippet: Detection of the relative expression of transcript level and protein level of each gene in UP group and Up + 5Azac group, Down group and Down + 5Azac group. a–b: At both transcriptional and protein levels, the Up + 5Azac group showed significantly lower DNMT3a/3b enzyme activities, higher PDGFA methylation levels, and increased COL1A1 and α-SMA expression compared to the Up group. c-d: At the transcriptional and protein levels, the Down + 5Azac group showed decreased DNMT3a/3b enzyme activity, increased PDGFA methylation levels, and increased COL1A1 and α-SMA expression compared to the Down group. Note: Up: exosomes overexpressing miRNA-29b were cocultured with LX-2 cells; Up + 5Azac: miRNA-29b -overexpressing exosomes + 5Azac were cocultured with LX-2 cells; Down: exosomes with low miRNA-29b expression were cocultured with LX-2 cells; Down + 5Azac: Exosomes with low expression of miRNA-29b + 5Azac were cocultured with LX-2 cells. a – d : LX-2 cells cocultured with exosomes from 6 independent experiments (n = 6). * indicates p < 0.05; ** indicates p < 0.01; *** indicates p < 0.001; **** indicates p < 0.0001

Article Snippet: The membrane was blocked with 5% skim milk and incubated with primary antibodies against DNMT3a, DNMT3b, PDGFA, COL1A1 and α-SMA (GeneTex, Abcam).

Techniques: Expressing, Methylation, Activity Assay

Journal: bioRxiv

Article Title: Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam

doi: 10.1101/2025.06.03.657600

Figure Lengend Snippet: (A) Venn diagrams illustrating the overlap between significantly dysregulated transcripts in three tissues. Names of the shared genes between all combinations of two tissues are indicated. (B) Heatmap detailing the extent of the log 2 fold changes in shared genes in all three tissues with blue for down and red for upregulated genes. The grey color represents transcript not detected in those tissues. Significant p-values are reported on the plots. * p-val<0.05,** p-val<0.01, and *** p-val<0.001. Significance was calculated using Quasi-likelihood F-test. (C) Bar charts showing the top significantly enriched terms in KEGG analysis of shared differentially expressed transcripts. The bar lengths report the significance of the enrichments, and the number of genes associated with each category is reported inside each bar. The red colour represents the significant terms (-log10(p-val) = 1.3). (D) Protein-protein network is formed by dysregulated transcripts that overlap between the tissues, as shown in (A). The 4 clusters, which are formed by the contribution of DEGs for all three tissues, are: (i) Ribosome/translation formed by Dhttip2 (B & L), Mrpl36 (SC & L), Mrpl14 (SC & L), Mrps21 (B & L), Rps4x (SC & L), Rpl34 (SC & L), Rps27rt (B & L) and Mettl17 (B & SC); (ii) RNA Splicing/transport: Ing4 (SC & L), Arid4b (B & L), Snrpa1 (SC & L), Stoml2 (B & L), Smn1 (B & SC), Ppie (SC & L) and Thoc7 (SC & L); (iii) DNA Replication: Mcm5 (B & L), Smc4 (B & L), Smc2 (SC & L), Tacc3 (SC & L); (iv) Extracellular matrix: Col1a1 (B & L), Col1a2 (B & L), Cdkn1a (SC & L) and Spp1 (B & SC). B stands for brain, SC for spinal cord and L for liver.

Article Snippet: Western blotting was performed using primary antibodies against Col1A1 (Proteintech 67288-1-Ig, 1:2500) and SMN (mouse anti-SMN, BD Biosciences 610647, 1:1,000).

Techniques:

Journal: bioRxiv

Article Title: Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam

doi: 10.1101/2025.06.03.657600

Figure Lengend Snippet: (A) Quantification of qPCR analysis performed for the Col1a1 transcripts in cytoplasmic mRNAs from control and SMA brain, spinal cord and liver at the P5, P10, and P18 stages of SMA disease in Smn 2B/- mice. Data are mean ± s.e.m. among n = 3 biologically independent samples. Significant changes were assessed using unpaired two-sided t-tests. (B) Relative co-sedimentation profile of Col1a1 mRNAs in control (grey) and SMA (red) brain, spinal cord and liver at P10. Data are mean ± s.e.m. among n = 3 biologically independent samples. Significant changes were assessed using unpaired two-sided Student’s t-tests. * p-val<0.05. Brain (p-value fraction 3 p = 0.01101). (C-E) Protein levels of Col1a1 and SMN in the brain (C), spinal cord (D), and liver (E) at P10 and P18 in controls and SMA using western blot analysis. Quantification of immunoblots for Col1a1 is normalized to total protein stain. SMA expression values were normalized and compared with control values for each of the tissues. Data are mean ± s.e.m. among n = 3 biologically independent samples. Significant changes were assessed using unpaired two-sided Student’s t-tests. * p-val<0.05 and ** p-val<0.01. Brain (p-value P18 p = 0.00794), Spinal cord (p-value P18 p =0.00219). (F,G) Quantification of qPCR analysis for Col1a1 and Col1a2 (F) relative co-sedimentation profile of Col1a1 and Col1a2 mRNAs and protein levels of Col1a1 (G) in the spinal cord and cortex tissues of a mouse model of Amyotrophic Lateral Sclerosis (blue) and littermate controls (grey). ( H ). Data are mean ± s.e.m. among n = 3 biologically independent samples. Significant changes were assessed using unpaired two-sided Student’s t-tests.

Article Snippet: Western blotting was performed using primary antibodies against Col1A1 (Proteintech 67288-1-Ig, 1:2500) and SMN (mouse anti-SMN, BD Biosciences 610647, 1:1,000).

Techniques: Control, Sedimentation, Western Blot, Staining, Expressing

Journal: bioRxiv

Article Title: Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam

doi: 10.1101/2025.06.03.657600

Figure Lengend Snippet: (A) COL1A1 mRNA levels in total RNA from healthy, carrier (H1-3 and C) and SMA patient-derived fibroblasts (P1-4, left). Data are mean ± s.e.m. among n = 3 independent technical replicates for each individual. Comparison between relative co-sedimentation profiles of COL1A1 mRNA from healthy (n=3) and SMA patient-derived fibroblasts SMA Type I (n = 2), SMA Type II (n = 2) (middle). Data are mean ± s.e.m. among n biological independent replicates. COL1A1 protein expression in healthy, carrier and SMA patient-derived fibroblasts (left), data are mean ± s.e.m. among n = 3 independent technical replicates. Expression values were normalized and compared with healthy control values. Significant changes between each healthy sample and the other samples were assessed using one-way ANOVA test, with Holm correction of p-values. Significant p-values are reported on the plots. (B, C) Comparison of COL1A1 protein expression in Coriell Institute cohort (Healthy n=3, SMA n=4) and UMCU cohort-paediatric (Healthy n=3, SMA n=6) and adult (Healthy n=5, SMA n=9). Data represent the mean ± s.e.m. of n individual, shown as a dot, for each group. Significant changes were assessed using unpaired two-sided Student’s t-tests. (D) Corelation between COL1A1/SMN protein expression and SMN2 copy number in SMA patients’ fibroblasts from the UMCU cohort. Data are plotted as mean of n=3 independent technical replicates. The regression line, its 99% confidence level interval, the Pearson correlation coefficient, and its p-value are displayed. Significant p-value<0.05 are highlighted in bold.

Article Snippet: Western blotting was performed using primary antibodies against Col1A1 (Proteintech 67288-1-Ig, 1:2500) and SMN (mouse anti-SMN, BD Biosciences 610647, 1:1,000).

Techniques: Derivative Assay, Comparison, Sedimentation, Expressing, Control

Journal: bioRxiv

Article Title: Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam

doi: 10.1101/2025.06.03.657600

Figure Lengend Snippet: (A) Schematic representation of the Risdiplam treatment. (B) Representative immunoblots for SMN in untreated (U) and Risdiplam-treated (R) patient-derived fibroblasts from 3 technical replicates of one paediatric patient and one healthy donor. The internal standard (Int. std.) is used to compare protein signal across different membranes. Each blot is accompanied by a corresponding total protein stain (lower panel). (C) Representative immunoblots for COL1A1 in untreated (U) and Risdiplam-treated (R) patient-derived fibroblasts from paediatric healthy donors, and paediatric and adult SMA patients. The internal standard (Int. std.) is used to compare protein signal across different membranes. Each blot is accompanied by a corresponding total protein stain (lower panel). (D) Quantification of SMN protein level of Risdiplam-treated (R) relative to the untreated (U) fibroblasts. Protein levels were normalized for total protein stain and internal standard. Data are mean ± s.e.m. among n = 3 technical independent replicates. Significant changes were assessed using unpaired two-sided Student’s t-test, with Holm correction of p-values. * p-val<0.05, ** p-val<0.01, *** p-val<0.001, and **** p-val<0.0001. (E) Quantification of COL1A1 protein level of Risdiplam-treated (R) relative to the untreated (U) fibroblasts. Protein levels were normalized for total protein stain and internal standard. Data are mean ± s.e.m. among n = 3 technical independent replicates. Significant changes were assessed using unpaired two-sided Student’s t-test, with Holm correction of p-values. * p-val<0.05, ** p-val<0.01, *** p-val<0.001, and **** p-val<0.0001.

Article Snippet: Western blotting was performed using primary antibodies against Col1A1 (Proteintech 67288-1-Ig, 1:2500) and SMN (mouse anti-SMN, BD Biosciences 610647, 1:1,000).

Techniques: Western Blot, Derivative Assay, Staining