Supplementary Tables 1 - 8, Figures 1 - 7 from Hypermethylation of the <i>GABRE∼miR-452∼miR-224</i> Promoter in Prostate Cancer Predicts Biochemical Recurrence after Radical Prostatectomy
Authors: Kristensen Helle , Haldrup Christa , Strand Siri , Mundbjerg Kamilla , Mortensen Martin M. , Thorsen Kasper , Ostenfeld Marie Stampe , Wild Peter J. , Arsov Christian , Goering Wolfgang , Visakorpi Tapio , Egevad Lars , Lindberg Johan , Grönberg Henrik , Høyer Søren , Borre Michael , Ørntoft Torben F. , Sørensen Karina D. 
Published: April 2023

<p>Supplemental Materials Part A: Supplementary Tables and Figures Part B: Supplementary Methods Supplementary Table S1. Clinicopathological characteristics of non-malignant and prostate cancer tissue samples used for bisulfite sequencing, Illumina 27K or 450K Infinium analysis Supplementary Table S2. GABRE expression in 9 independent PC datasets available from the ONCOMINE database Supplementary Table S3: Genes downregulated more than 0.5 fold (log2) in both PC3 and DU145 cells when overexpressing miR-224 compared to scrambled transfected cells (only genes with crosshyb_type = 1 were considered). Supplementary Table S4: Genes downregulated more than 0.5 fold (log2) in both PC3 and DU145 cells when overexpressing miR-452 compared to scrambled transfected cells (only genes with crosshyb_type = 1 were considered). Supplementary Table S5. Shortlist of potential miR-224 and miR-452 target genes Supplementary Table S6. Uni- and multivariate Cox regression analyses of biochemical recurrence-free survival in two RP cohorts. Supplementary Table S7. Uni- and multivariate Cox regression analysis of GABRE, miR-224, and miR-452 expression in relation to biochemical recurrence-free survival in the Taylor et al. RP cohort. Supplementary Table S8. Uni- and multivariate Cox regression analysis of GABRE/miR-452/miR-224 and OAZ2 (predicted miR-452 target) gene expression in relation to biochemical recurrence-free survival in the Taylor et al. RP cohort. Supplementary Figure S1. Flow charts describing sample inclusion/exclusion criteria. Supplementary Figure S2. Positive correlations between miR-224, miR-452, and GABRE expression Supplementary Figure S3. Methylation patterns of 52 CpG sites in the GABRE~miR-452~miR-224 promoter associated CpG island determined by bisulfite sequencing of prostate tissue samples from adjacent non-malignant (AN, n=7), benign prostatic hyperplasia (BPH, n=4), localized PC (LPC, n=10), and primary tumor samples from patients with metastatic PC (MPC, n=10). Supplementary Figure S4. A. Bisulfite sequencing of 52 CpG sites in the GABRE promoterassociated CpG island in three nonmalignant (PrEC, BPH1, PNT1A) and six prostate cancer cell lines (22rv1, LNCaP, VCaP, DuCaP, DU145, PC3). Supplementary Figure S5. 450K Infinium data for the GABRE~miR-224~miR-452 locus and neighboring genes at Xq28. Supplementary Figure S6. Gene-set Enrichment Analysis of "Canonical Pathways" for genes down/upregulated in DU145 or PC3 cells after miR-224 or miR-452 transfection, respectively (compared to non/scr-transfected cells and corrected for transfection-related non-specific effects). Supplementary Figure S7. Association between GABRE/MYOD1 methylation levels and clinicopathological parameters in two RP patient cohorts.</p>