Journal: BMC Cancer
Article Title: AP-2α gene deregulation is associated with renal cell carcinoma patient survival
doi: 10.1186/s12885-024-12526-w
Figure Lengend Snippet: COBRA methylation analysis of the AP-2α gene in different subtypes of RCC. A , Venn diagram depicted the number of genes identified as methylated for 19 clear cell RCC, 4 papillary RCC and 4 chromophobe RCC. B , Snapshot views from Signalmap of AP-2α gene showed the transcription start site (TSS, position:10,523,256), CpG islands (gray column) and methylation area (black column) of these regions from the RCC samples. The data showed the methylation status of the representative 2 clear cell RCC, 2 chromophobe RCC, 2 papillary RCC, and 2 oncocytoma RCC. The arrow indicated the transcription direction of AP-2α gene. C , Schematic representation of CpG distribution in the exon 2 region of the human AP-2α gene. A total of 22 CpG dinucleotides were analyzed in the indicated region (vertical tick mark). Bisulfite PCR primers (arrows) were designed with Methyl Primer Express ® Software v1.0 and used to amplify DNA from different subtypes of RCC tumor specimens. 3 Bst UI cutting sites were included in the amplified fragment. D , Methylation analysis by COBRA for different paired RCC tumor (T) and adjacent nontumor tissue samples (N) was performed, and the representative results are shown. We used CpGenome universal methylated DNA as a positive control (C) for methylation studies. Arrows indicate unmethylated (U)/methylated (M) alleles. E , The methylation status of different subtypes of RCC was analyzed using the COBRA approach. 47 clear cell, 8 papillary, 9 chromophobes, and 3 other (2 granular and 1 unclassified) RCC clinical tumor samples were included in this experiment
Article Snippet: The methyl primers obtained from Methyl Primer Express® Software v1.0 (Applied Biosystems Inc., Foster City, CA, USA) in COBRA were AP-2α methyl-1 forward primer (5’-GGTATTTTTTTTGGGGTAGGTA-3’) and reverse primer (5’-TACAACCTAAACCCCCTACAC-3’).
Techniques: Combined Bisulfite Restriction Analysis Assay, Methylation, Software, Amplification, Positive Control
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