Table 5. Hypermethylated genes in the Small Airway Epithelium (SAE) of waterpipe smokers vs nonsmokers with corresponding changes in gene expression1.
| Gene | HELP assay | U133 gene expression | ||||
|---|---|---|---|---|---|---|
| Probeset | Fold-change2 | p value | Probeset | Fold-change3 | p value | |
| Up-regulated gene expression | ||||||
| HLA-DQA1 | chr6:32604793–32605702 | 4.19 | 5.2x10-3 | 213831_at | 8.45 | 3.6x10-2 |
| HLA-DQB1 | chr6:32631147–32632209 | 1.77 | 8.2x10-4 | 209480_at | 8.20 | 3.5x10-2 |
| EIF2S1 | chr14:67825081–67825321 | 2.08 | 1.5x10-2 | 201143_s_at | 2.76 | 1.9x10-2 |
| ABCC3 | chr17:48711832–48712151 | 3.04 | 4.1x10-3 | 208161_s_at | 1.57 | 1.8x10-2 |
| CDK10 | chr16:89755670–89755932 | 1.80 | 1.4x10-2 | 203468_at | 1.46 | 2.3x10-2 |
| FAM115A | chr7:143581612–143582257 | 1.53 | 3.6x10-2 | 204403_x_at | 1.43 | 5.7x10-3 |
| COL16A1 | chr1:32170869–32171297 | 2.04 | 4.2x10-2 | 204345_at | 1.37 | 3.3x10-2 |
| PRKAG2 | chr7:151573964–151574355 | 3.22 | 3.2x10-2 | 215231_at | 1.35 | 1.6x10-2 |
| TMC5 | chr16:19474685–19475411 | 1.56 | 4.6x10-2 | 240303_at | 1.32 | 2.8x10-2 |
| RAP1GAP | chr1:21995005–21995517 | 2.29 | 4.2x10-2 | 210618_at | 1.32 | 2.2x10-2 |
| CNPY2 | chr12:56709384–56709713 | 1.80 | 4.6x10-2 | 209797_at | 1.30 | 8.9x10-3 |
| ASPHD2 | chr22:26824590–26825080 | 1.62 | 3.8x10-2 | 227015_at | 1.28 | 3.7x10-2 |
| CISD2 | chr4:103789518–103790086 | 1.60 | 5.9x10-3 | 244275_at | 1.26 | 1.4x10-2 |
| SF3B1 | chr2:198243286–198243955 | 1.58 | 1.7x10-2 | 211185_s_at | 1.25 | 2.2x10-2 |
| FAN1 | chr15:31109598–31110925 | 1.62 | 1.1x10-2 | 239289_x_at | 1.23 | 3.7x10-2 |
| FGF1 | chr5:141991981–141992881 | 1.53 | 1.7x10-2 | 205117_at | 1.22 | 3.1x10-2 |
| RARG | chr12:53614211–53614816 | 2.62 | 3.0x10-2 | 217178_at | 1.21 | 3.8x10-2 |
| STAMBP | chr2:74055331–74056076 | 1.66 | 3.2x10-2 | 235361_at | 1.20 | 4.2x10-2 |
| EIF2AK4 | chr15:40227738–40228469 | 1.89 | 1.6x10-2 | 225164_s_at | 1.20 | 4.9x10-2 |
| FLJ39739 | chr1:147931322–147931613 | 2.08 | 4.5x10-2 | 239005_at | 1.18 | 2.4x10-2 |
| CDKL2 | chr4:76554977–76556043 | 2.37 | 7.8x10-3 | 236331_at | 1.18 | 4.8x10-2 |
| TTC17 | chr11:43380706–43381027 | 2.00 | 4.9x10-2 | 224849_at | 1.17 | 3.6x10-2 |
| POLR3E | chr16:22308202–22308674 | 1.76 | 2.7x10-2 | 233458_at | 1.16 | 2.4x10-2 |
| AKAP8 | chr19:15490443–15490780 | 2.58 | 3.2x10-2 | 203848_at | 1.13 | 7.4x10-3 |
| LSM14A | chr19:34663415–34663678 | 1.85 | 4.0x10-2 | 222099_s_at | 1.12 | 4.0x10-2 |
| Down-regulated gene expression | ||||||
| PTPRS | chr19:5339127–5339748 | 2.27 | 2.9x10-2 | 1555666_at | -1.10 | 3.8x10-2 |
| FBXO22 | chr15:76196310–76196551 | 1.97 | 1.8x10-2 | 225736_at | -1.14 | 2.6x10-2 |
| PRICKLE3 | chrX:49043787–49044009 | 1.54 | 2.4x10-3 | 217349_s_at | -1.14 | 4.9x10-2 |
| LOC100129716 | chr5:90576485–90577374 | 3.05 | 4.4x10-2 | 239395_at | -1.14 | 3.5x10-2 |
| ZNF384 | chr12:6798919–6799942 | 1.70 | 1.2x10-2 | 212369_at | -1.17 | 1.6x10-2 |
| SIRPA | chr20:1876115–1876469 | 1.81 | 4.0x10-2 | 202895_s_at | -1.18 | 2.5x10-2 |
| FZD1 | chr7:90894525–90894849 | 2.06 | 4.2x10-2 | 204452_s_at | -1.19 | 1.6x10-2 |
| SPANXC | chrX:140336315–140336567 | 1.52 | 5.0x10-2 | 220217_x_at | -1.21 | 4.5x10-3 |
| WDR33 | chr2:128568380–128568877 | 2.57 | 4.9x10-2 | 222763_s_at | -1.21 | 2.4x10-3 |
| LOC642597 | chr18:5197186–5197418 | 1.71 | 4.4x10-2 | 243506_at | -1.22 | 3.6x10-2 |
| RPL26 | chr17:8287040–8287521 | 1.64 | 1.9x10-2 | 222229_x_at | -1.23 | 6.6x10-3 |
| RAB4B | chr19:41284200–41284788 | 3.37 | 4.7x10-2 | 233385_x_at | -1.25 | 2.8x10-2 |
| JARID2 | chr6:14738030–14739232 | 1.50 | 1.4x10-2 | 203298_s_at | -1.26 | 4.7x10-2 |
| FBXL22 | chr15:63893258–63893671 | 3.29 | 3.8x10-2 | 241350_at | -1.26 | 9.5x10-4 |
| ZSCAN10 | chr16:3142746–3143151 | 1.95 | 4.5x10-2 | 1553875_s_at | -1.28 | 3.7x10-2 |
| RPS15 | chr19:1438945–1439352 | 1.81 | 3.3x10-2 | 200819_s_at | -1.29 | 3.8x10-3 |
| NDUFS8 | chr11:67797997–67798357 | 1.91 | 4.7x10-2 | 203189_s_at | -1.30 | 2.0x10-2 |
| ATP6V1D | chr14:67825081–67825321 | 2.08 | 1.5x10-2 | 208898_at | -1.32 | 2.4x10-4 |
| QDPR | chr4:17511919–17512817 | 1.66 | 8.9x10-3 | 209123_at | -1.38 | 2.0x10-2 |
| SNRPB | chr20:2448332–2449291 | 2.05 | 1.5x10-2 | 213175_s_at | -1.39 | 3.2x10-2 |
| CBX4 | chr17:77815106–77815348 | 2.39 | 4.7x10-2 | 206724_at | -1.50 | 1.2x10-2 |
| KGFLP1 | chr9:41998251–41999298 | 1.58 | 1.6x10-2 | 1554741_s_at | -1.51 | 2.2x10-2 |
| RAB4A | chr1:229406326–229406592 | 1.54 | 3.8x10-2 | 203582_s_at | -1.52 | 1.3x10-2 |
| C1orf88 | chr1:111888875–111889467 | 1.84 | 1.6x10-2 | 228100_at | -1.52 | 4.7x10-3 |
| PA2G4 | chr12:56498194–56498668 | 2.96 | 2.1x10-2 | 214794_at | -1.52 | 2.9x10-2 |
| UCKL1 | chr20:62583662–62583944 | 2.41 | 4.5x10-2 | 232675_s_at | -1.54 | 9.5x10-3 |
| UQCC | chr20:34000302–34000646 | 2.04 | 1.2x10-2 | 222470_s_at | -1.84 | 1.5x10-2 |
| HBA1 | chr16:227144–228315 | 1.53 | 4.6x10-2 | 214414_x_at | -8.38 | 4.6x10-2 |
1 Hypermethylated genes in the SAE of waterpipe smokers compared to nonsmokers with corresponding changes in gene expression. Genes are listed based on fold-change of gene expression.
2 Fold-change in HELP assay. Negative fold-change represents hypomethylation and positive fold-change represents hypermethylation.
3 Fold-change in U133 gene expression. Positive fold-change represents increased gene expression and negative fold-change represents decreased gene expression.