Table 2.
Associations of LAG3 methylation and mRNA expression (mean levels) with VHL, PBRM1, SETD2, KDM5C, and BAP1 mutation status in KIRC
| Analyte (CpG site/bead, mRNA) | Number | VHL | PBRM1 | SETD2 | KDM5C | BAP1 | ||||||||||
| Wild type (n=179) | Mutant (n=140) |
P value | Wild type (n=228) |
Mutant (n=91) |
P value | Wild type (n=287) |
Mutant (n=32) |
P value | Wild type (n=301) |
Mutant (n=18) |
P value | Wild type (n=296) |
Mutant (n=23) |
P value | ||
| LAG3 mRNA | NA | 6.481 | 6.68 | 0.36 | 6.717 | 6.19 | 0.028 | 6.58 | 6.42 | 0.65 | 6.56 | 6.65 | 0.86 | 6.51 | 7.34 | 0.045 |
| cg26956535 | 1 | 88.4 | 88.1 | 0.76 | 88.3 | 88.1 | 0.80 | 89.2 | 79.7 | <0.001 | 88.3 | 86.8 | 0.41 | 88.3 | 87.7 | 0.72 |
| cg22777668 | 2 | 23.8 | 22.1 | 0.07 | 23.6 | 21.7 | 0.073 | 23.4 | 20.2 | 0.035 | 23.3 | 18.5 | 0.014 | 23.0 | 23.1 | 0.98 |
| cg16352928 | 3 | 65.5 | 66.0 | 0.67 | 64.4 | 69.0 | 0.002 | 66.0 | 63.5 | 0.28 | 65.8 | 64.3 | 0.61 | 66.3 | 58.1 | 0.002 |
| cg02695343 | 4 | 65.3 | 65.1 | 0.91 | 64.1 | 68.1 | 0.007 | 65.6 | 61.6 | 0.079 | 65.3 | 63.4 | 0.52 | 65.9 | 57.0 | 0.001 |
| cg10500147 | 5 | 59.3 | 59.2 | 0.97 | 57.8 | 63.0 | 0.010 | 60.0 | 53.2 | 0.026 | 59.4 | 56.7 | 0.48 | 60.0 | 50.3 | 0.006 |
| cg17213699 | 6 | 78.3 | 77.9 | 0.83 | 76.9 | 81.1 | 0.021 | 78.6 | 74.1 | 0.097 | 78.3 | 75.7 | 0.46 | 78.8 | 69.0 | 0.002 |
| cg19872463 | 7 | 73.8 | 73.8 | 0.97 | 72.6 | 76.9 | 0.023 | 74.3 | 69.1 | 0.068 | 73.9 | 72.1 | 0.62 | 74.4 | 66.4 | 0.016 |
| cg04671742 | 8 | 78.2 | 78.6 | 0.67 | 77.5 | 80.6 | 0.006 | 78.2 | 80.1 | 0.26 | 78.4 | 77.7 | 0.73 | 78.7 | 75.0 | 0.06 |
| cg01820374 | 9 | 39.2 | 40.2 | 0.39 | 38.6 | 42.3 | 0.002 | 39.8 | 38.1 | 0.36 | 39.9 | 35.7 | 0.08 | 39.6 | 39.4 | 0.91 |
| cg19421125 | 10 | 76.1 | 76.9 | 0.51 | 75.5 | 78.9 | 0.008 | 76.4 | 77.3 | 0.66 | 76.6 | 74.8 | 0.48 | 77.1 | 69.3 | 0.001 |
| cg10191002 | 11 | 61.1 | 62.2 | 0.24 | 60.8 | 63.3 | 0.015 | 61.6 | 61.3 | 0.88 | 61.6 | 60.9 | 0.72 | 62.0 | 56.4 | 0.002 |
| cg20652042 | 12 | 76.4 | 76.4 | 0.95 | 75.6 | 78.4 | <0.001 | 76.3 | 77.2 | 0.46 | 76.4 | 76.8 | 0.79 | 76.6 | 74.8 | 0.19 |
| cg06157570 | 13 | 74.7 | 76.2 | 0.10 | 74.4 | 77.8 | 0.001 | 75.2 | 76.5 | 0.40 | 75.6 | 70.8 | 0.015 | 75.0 | 79.5 | 0.012 |
| cg14292870 | 14 | 37.6 | 36.3 | 0.35 | 38.2 | 34.1 | 0.005 | 37.3 | 34.6 | 0.23 | 37.3 | 33.3 | 0.17 | 36.5 | 44.0 | 0.003 |
| cg11429292 | 15 | 16.9 | 17.9 | 0.32 | 18.1 | 15.5 | 0.018 | 17.5 | 15.7 | 0.27 | 17.3 | 17.5 | 0.94 | 17.0 | 22.4 | 0.005 |
| cg15828668 | 16 | 5.6 | 5.4 | 0.31 | 5.7 | 5.2 | 0.13 | 5.6 | 5.2 | 0.46 | 5.5 | 5.2 | 0.62 | 5.5 | 5.2 | 0.53 |
LAG3 methylation was determined at 16 different CpG sites targeted by HumanMethylation450 BeadChip beads (figure 1). Significant data are shown in boldface.
KIRC, clear cell renal cell carcinoma; LAG3, lymphocyte activating 3; NA, not applicable.