American Association for Cancer Research
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Supplementary Tables S1-11 from Tumor-Suppressive miR148a Is Silenced by CpG Island Hypermethylation in IDH1-Mutant Gliomas

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posted on 2023-03-31, 18:30 authored by Sichen Li, Reshmi Chowdhury, Fei Liu, Arthur P. Chou, Tie Li, Reema R. Mody, Jerry J. Lou, Weidong Chen, Jean Reiss, Horacio Soto, Robert Prins, Linda M. Liau, Paul S. Mischel, Phioanh L. Nghiemphu, William H. Yong, Timothy F. Cloughesy, Albert Lai

Supplementary Tables S1-11. Supplementary Table S1. Patient demographics of the RRBS discovery set. Supplementary Table S2. RRBS Mean Coverage per sample. Supplementary Table S3. RRBS coverage of CpG islands associated with miRNAs. Supplementary Table S4. Hypermethylated CpG islands within 5000 bp of miRNAs in IDH1MUT versus IDH1/2WT gliomas (G-CIMP). Supplementary Table S5. Targeted bisulfite sequencing results for miR-148a associated CpG island (Region 1). Supplementary Table S6. Targeted bisulfite sequencing results for miR-148a associated CpG island (Region 2). Supplementary Table S7. Demographics and miR-148a methylation status of GBM and Grade III glioma patient cohort. Supplementary Table S8. Univariate and Multivariate Cox Proportional Hazards Analysis of Factors Affecting OS in GBM and Grade III gliomas. Supplementary Table S9. Predicted miR-148a targets. Supplementary Table S10. Bisulfite sequencing primer sets. Supplementary Table S11. Methylation Specific PCR (MSP) primer sets.



Purpose:IDH1/2-mutant gliomas harbor a distinct glioma-CpG island methylation phenotype (G-CIMP) that may promote the initiation and progression of secondary pathway gliomas by silencing tumor-suppressive genes. The potential role of tumor-suppressive microRNAs (miRNA; miR) in this process is not understood.Experimental Design: To identify potential tumor-suppressive miRNA hypermethylated in glioma, the methylation profiles of IDH1/2WT gliomas (n = 11) and IDH1MUT glioma (n = 20) were compared by using massively parallel reduced representation bisulfite sequencing (RRBS). The methylation status of selected miRNA was validated by using targeted bisulfite sequencing (BiSEQ) in a large cohort of glioma tissue samples including 219 IDH1WT and 72 IDH1/2MUT samples. The expression of selected miRNAs was determined by using the TaqMan qPCR. Functional analyses of miR148a were conducted and target genes were identified.Results: We identify miR148a as a novel, G-CIMP–associated miRNA whose methylation is tightly correlated with IDH1 mutation and associated with improved survival in patients with malignant glioma. We confirm that downregulation of miR148a can occur via DNA methylation. We demonstrate that IDH1 mutation provides a mechanism of miR148a methylation and downregulation, and that restoration of miR148a reduced tumorigenic properties of glioma cells, possibly by targeting DNMT1.Conclusions: We identify miR148a as a novel G-CIMP–associated miRNA, and provide results suggesting that miR148a restoration may have therapeutic implications. Clin Cancer Res; 20(22); 5808–22. ©2014 AACR.