Table 1.
Patient and tumor characteristics.
Figure 1.
Hierarchical Clustering of DNA methylation in 24 PA cases.
The HM450 probes (7,674) with the highest 2% of standard deviation across the set of 383,718 global HM450 probes were used.
Figure 2.
Global CpG DNA methylation profiles in PAs.
A, Comparison of mean DNA methylation levels across 383,718 HM450 probes in noninvasive (Knosp grade 0, 1) and invasive (Knosp grade 2, 3, 4) PAs. B, Mean DNA methylation levels in PA cases across the five different Knosp grades (0–4) among the set of 383,718 HM450 probes. C, Comparison of mean DNA methylation levels across 383,718 HM450 probes in FAs and NFAs. P-value was calculated via simple t-test. D, Comparison of mean DNA methylation levels across 383,718 HM450 probes in only NFAs. P-value was calculated via simple t-test. All of the above DNA methylation beta values are shown as mean ± SEM in different groups. E and F, DNA methylation levels in gene regions (TSS1500, TSS200, 5′UTR, 1stExon, gene body and 3′UTR) for NFAs (panel E) and FAs (Panel F). TSS200: 200 bp within transcription start site; TSS1500: 1500 bp within transcription start site; UTR: untranslated region; 1stExon: the first exon of gene.
Figure 3.
Characteristics of significantly methylated CpG sites in PA cases.
Whiskers were used to represent the min to max beta values. A-D, Panel of 3,072 CpG sites located in Ref-Seq genes were interrogated for their DNA methylation in NFAs compared to FAs for all probes and stratified by location relative to each gene region and CpG density. A, The distribution of differentially methylated CpGs across different gene related regions. B, Stratified by CpG density. CpG islands (CGI), CpG island shores (0–2 kb from island edge, N and S indicate the upstream and downstream of the island, respectively), CpG island shelves (0–2 kb from shore edge, N and S indicate the upstream and downstream of the island, respectively) and non-CpG island probes. C and D, Relative distribution and count of the promoter associated CpGs (total 360), which were singled out from the global significant CpG sites (total 3027). E, KCNAB2 (cg18192083) MethyLight assay in NFA and FA, which was consistent with the genome-wide DNA methylation analysis.
Table 2.
Top 30 significant genes with differential DNA methylation between NFAs and FAs.
Figure 4.
A, Linear regression analysis showed negative trend of DNA methylation and gene expression. B, Three overlapped significant genes of DNA methylation and gene expression when compared NFAs to FAs. C, gene ODAM expression in one FA subject of d0079 which secreted hormones of GH and TSH, GAPDH gene expression was used as control.
Table 3.
List of genes with most significant differences in expression between NFAs and FAs.