Table 2.
Methylation status intensity in tumor suppressor genes in breast cancer
| All Samples | Cluster Groups | |||||||
|---|---|---|---|---|---|---|---|---|
|
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| Gene Promoters | n = 98 | Highly Methylated n = 16 | Sparsely Methylated n = 82 | Differences of the means | ||||
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| ¥ ± SD | (% MS) | ¥ ± SD | (% MS) | ¥ ± SD | (% MS) | Highly-Sparsely | ||
| APC | 36.3 ± 27.4 | 83 | 53.8 ± 28.0 | 94 | 32.9 ± 26.1 | 80 | 20.8 | |
| ATM | 15.7 ± 23.9 | 46 | 56.7 ± 20.3 | 100 | 7.6 ± 14.4 | 35 | 49.0 | |
| BRCA1 | 5.7 ± 16.2 | 15 | 13.5 ± 25.7 | 38 | 4.2 ± 13.3 | 11 | 9.3 | |
| BRCA2 | 3.2 ± 11.5 | 12 | 12.7 ± 25.3 | 25 | 1.4 ± 4.5 | 10 | 11.3 | |
| CASP8* | 7.1 ± 13.2 | 31 | 16.8 ± 15.9 | 69 | 5.2 ± 11.8 | 23 | 11.6 | |
| CD44 | 1.0 ± 7.2 | 2 | 2.4 ± 9.5 | 6 | 0.7 ± 6.7 | 1 | 1.6 | |
| CDH13 | 26.1 ± 21.9 | 78 | 36.1 ± 22.5 | 81 | 24.2 ± 21.3 | 77 | 11.9 | |
| CDKN1B | 6.4 ± 18.6 | 15 | 33.1 ± 35.2 | 56 | 1.2 ± 4.3 | 7 | 32.0 | |
| CDKN2A | 14 ± 23.1 | 45 | 51.1 ± 33.2 | 81 | 6.7 ± 10.4 | 38 | 44.4 | |
| CDKN2B | 3.5 ± 11.7 | 11 | 17.3 ± 23.6 | 44 | 0.8 ± 4.0 | 5 | 16.5 | |
| CHFR | 9.1 ± 18.9 | 26 | 38.5 ± 25.9 | 88 | 3.3 ± 9.9 | 13 | 35.2 | |
| DAPK1* | 9.6 ± 19.5 | 24 | 34.6 ± 27.6 | 69 | 4.8 ± 12.8 | 16 | 29.9 | |
| ESR1 | 3.3 ± 14.2 | 8 | 15.9 ± 31.8 | 25 | 0.8 ± 3.9 | 5 | 15.2 | |
| FHIT | 4.3 ± 15.1 | 10 | 22.8 ± 31.1 | 44 | 0.7 ± 3.6 | 4 | 22.1 | |
| GSTP1* | 16.3 ± 26.9 | 40 | 28.4 ± 38.8 | 44 | 13.9 ± 23.5 | 39 | 14.6 | |
| HIC1 | 5.9 ± 20.1 | 12 | 31.4 ± 41.1 | 44 | 0.9 ± 3.9 | 6 | 30.4 | |
| IGSF4 | 3.2 ± 10.8 | 10 | 13.1 ± 20.9 | 31 | 1.2 ± 5.9 | 6 | 11.9 | |
| MLH1 | 3.9 ± 10.5 | 15 | 15.9 ± 16.6 | 62 | 1.6 ± 6.9 | 6 | 14.4 | |
| PTEN | 3.9 ± 7.8 | 26 | 9.4 ± 14.3 | 38 | 2.8 ± 5.3 | 23 | 6.6 | |
| RARB | 2.7 ± 10.0 | 8 | 3.8 ± 10.7 | 12 | 2.4 ± 9.9 | 7 | 1.3 | |
| RASSF1* | 37.5 ± 28.5 | 79 | 49.2 ± 35.0 | 81 | 35.3 ± 26.7 | 78 | 14.0 | |
| TIMP3 | 3.9 ± 12.7 | 12 | 5.8 ± 16.3 | 12 | 3.6 ± 12 | 12 | 2.2 | |
| TP73 | 4.0 ± 14.1 | 13 | 18.5 ± 30.5 | 31 | 1.2 ± 3.9 | 10 | 17.3 | |
| VHL | 8.1 ± 23.8 | 13 | 41.3 ± 44.7 | 50 | 1.6 ± 6.8 | 6 | 39.7 | |
|
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| TOTAL METHYLATED GENES PER PATIENT | Mean (SD) | 5.97 (3.7) | 12.1 (2.9) | 4.8 (2.5) | ||||
| Median (Q1-Q3) | 5.0 (3.25-8.0) | 11.5 (10.0-15.0) | 4.0 (3.0-6.0) | |||||
¥Mean methylation percentage; % MS: Percentage of Methylated samples; SD: Standard deviation; In bold are indicated genes that show major differences between highly and sparsely methylated; groups;
*
genes whose methylation is associated with an increased percentage of CNA in the tumors.