Journal: bioRxiv

Article Title: RNAMaRs: an interpretable framework for inferring multivalent RNA Motifs and cognate Regulators of Splicing

doi: 10.64898/2026.01.31.703040

Figure Lengend Snippet: A. Distribution of differentially spliced CEs classified as constitutive, enhanced, or silenced following HNRNPK depletion in PC3 cells. B-C. RNAMaRs summary visualizations for enhanced (B) and silenced (C) exons, showing region-specific normalized binding scores (BSs), association scores (ASs) between MRMs and candidate RBPs, and RNA splicing maps. D. Sequence logos summarizing enriched MRMs in silenced exons associated with HNRNPK across datasets. Barplot reports positional similarities between the two PWMs measured as Pearson Correlation Coefficients (PCC). E. Venn diagram representing the intersection of MRMs enriched in silenced exons between PC3 and HepG2 cell lines. F. Sequence logos summarizing MRMs shared and private between cell lines. G. MRM-specific RNA splicing maps for silenced exons in the two cell lines.

Article Snippet: PC3 cells (ATCC CRL-7934; RRID: CVCL_0035) were obtained from ATCC, and cell line identity was verified by short tandem repeat (STR) profiling (DDC Medical).

Techniques: Binding Assay, Sequencing

Journal: Cellular & Molecular Biology Letters

Article Title: Methylation-induced silencing of AZGP1 enhances prostate cancer metastasis by stimulating tumoral glycolysis

doi: 10.1186/s11658-025-00818-3

Figure Lengend Snippet: Lower AZGP1 expression facilitates the progression and prognosis of PCa. A Boxplot of the differences in AZGP1 expression among PCa samples with T2, T3, and T4 stages in the TCGA-PRAD dataset. B Boxplot of the differences in AZGP1 expression between N0 and N1 PCa samples in the TCGA-PRAD dataset. C Boxplot of the differences in AZGP1 expression among PCa samples with different Gleason scores in the TCGA-PRAD dataset. D Forest plot visualizing the meta-analysis of nine bulk datasets based on the Cox regression analysis of AZGP1 expression. E In vivo imaging of six OE- Azgp1 and six NC mice (left) with tail vein injections of PC3 cells. Comparison of the average immunofluorescence intensity of the metastatic regions (right). F Representative images of immunohistochemical staining for AZGP in metastatic and non-metastatic PCa tissue samples. G Scatter plots comparing the histoscores (H-score) of the immunohistochemical staining between 20 metastatic and 20 non-matastatic PCa tissue samples. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001

Article Snippet: The cell lines used in the experiment included the PCa cell lines PC3, DU145, LNCaP, 22RV1, and RM-1, which were obtained from the American Type Culture Collection (ATCC).

Techniques: Expressing, In Vivo Imaging, Comparison, Immunofluorescence, Immunohistochemical staining, Staining

Journal: Cellular & Molecular Biology Letters

Article Title: Methylation-induced silencing of AZGP1 enhances prostate cancer metastasis by stimulating tumoral glycolysis

doi: 10.1186/s11658-025-00818-3

Figure Lengend Snippet: AZGP1 regulates the cell proliferation and migration of PCa cells. A Relative expression of AZGP1 in seven prostate epithelial cell lines in the Cancer Cell Line Encyclopedia (CCLE) database. B Relative expression of AZGP1 in five human prostate epithelial cell lines: 22RV1, LNCaP, PC3, and DU145. C qRT-PCR analyses of AZGP1 mRNA in PC3 cells treated with negative control (NC) or AZGP1 pcDNA. qRT-PCR analyses of AZGP1 mRNA in 22RV1 cells treated with negative control (NC) or AZGP1 siRNA (siRNA1, siRNA2, and siRNA3). D Transwell assays assessed cell migration and invasion in 22RV1 cells upon AZGP1 knockdown. E Transwell assays assessed cell migration and invasion in PC3 cells upon AZGP1 overexpression. F , G Wound healing assays evaluated the migration of 22RV1 and PC3 cells. H Western blot analysis of the protein levels of N-cadherin, E-cadherin, VEGFA, MMP7, and AZGP1 after AZGP1 was overexpressed in PC3 cells and was knocked down in 22RV1 cells. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001

Article Snippet: The cell lines used in the experiment included the PCa cell lines PC3, DU145, LNCaP, 22RV1, and RM-1, which were obtained from the American Type Culture Collection (ATCC).

Techniques: Migration, Expressing, Quantitative RT-PCR, Negative Control, Knockdown, Over Expression, Western Blot

Journal: Cellular & Molecular Biology Letters

Article Title: Methylation-induced silencing of AZGP1 enhances prostate cancer metastasis by stimulating tumoral glycolysis

doi: 10.1186/s11658-025-00818-3

Figure Lengend Snippet: Decreased expression of AZGP1 activates the glycolytic pathway. A Bar plots showing the differential enrichment of KEGG metabolism pathways between LM and primary cancer cells derived from scMetabolism analyses in scRNA-seq data. B Correlation plot of AZGP1 expression with the ssGSEA score of the glycolysis pathway. C , D Correlation plots of AZGP1 expression with expression of the glycolytic enzymes LDHA and GP1 . E–G Boxplot of lactic acid production, basal OCR, and ECAR detection in PC3 and OE- AZGP1 PC3 cells. H – J Boxplot of lactic acid production, basal OCR, and ECAR detection in 22RV1 and si-22RV1 cells. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001

Article Snippet: The cell lines used in the experiment included the PCa cell lines PC3, DU145, LNCaP, 22RV1, and RM-1, which were obtained from the American Type Culture Collection (ATCC).

Techniques: Expressing, Derivative Assay

Journal: Cellular & Molecular Biology Letters

Article Title: Methylation-induced silencing of AZGP1 enhances prostate cancer metastasis by stimulating tumoral glycolysis

doi: 10.1186/s11658-025-00818-3

Figure Lengend Snippet: Differential promoter region methylation regulates AZGP1 expression in PCa metastasis. A The regulatory model diagram of AZGP1 promoter methylation and gene expression (upper). Correlation of DNA methylation changes at promoter and gene expression levels (left lower). Correlation of DNA methylation changes at promoter and methyltransferases (right lower). B Boxplot of cg26429636 methylation level between N0 and N1 PCa in the TCGA-PRAD database. C Boxplot of cg26429636 methylation levels between M0 and M1 PCa in the TCGA-PRAD database. D–F Scatter plot of correlations between the mRNA level of AZGP1 and methyltransferases, including DNMT1, DNMT3A, and DNMT3B. G–L Scatter plot of correlations between cg26429636 methylation level and methyltransferase expression, including DNMT1, DNMT3A, and DNMT3B. M Methylation-specific PCR (MSP) analysis of the methylation status of AZGP1 shows aberrant methylation in 22RV1, LNCaP, PC3, and DU145 cell lines. “M” and “U” represent MSP results using primer sets for methylated and unmethylated AZGP1 genes, respectively. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001

Article Snippet: The cell lines used in the experiment included the PCa cell lines PC3, DU145, LNCaP, 22RV1, and RM-1, which were obtained from the American Type Culture Collection (ATCC).

Techniques: Methylation, Expressing, Gene Expression, DNA Methylation Assay