Table 3.
Details of some candidate hypermethylated genes in AR positive and AR negative prostate cancer cell lines as compared to normal cell line.
| Gene Name | Methylation Fold in AR positive (LNCaP) compared to RWPE1 |
Mean±SD methylation Fold in AR negative compared to RWPE1 |
Description of Gene | Chromosome location |
|---|---|---|---|---|
| Tumor Suppressor Genes | ||||
| TMS-1 | 17.7 | 9.47±3.68 | Target of methylation – induced silencing 1 |
16p12-p11.2 |
| 14-3-3 sigma | 16.7 | 15.42±2.80 | 1p36.11 | |
| RB | 19.2 | 19.62±3.55 | Retinoblastoma | 13q14.2 |
| RBL1 | 20.9 | 14.64±1.61 | Retinoblastoma like 1 | 20q11.2 |
| PAX6 | 12.2 | 17.81±2.12 | Paired box gene 6 | 11p13 |
| DAPK | 18.7 | 10.89±5.86 | Death associated protein kinases |
9q34.1 |
| SRBC | 12.4 | 12.94±1.12 | Protein kinase C, delta binding protein |
11p15.4 |
| MASPIN | 6.2 | 6.68±0.91 | protease inhibitor 5 | 18q21.3 |
| Transcription Factors | ||||
| STAT1 | 17.6 | 7.59±2.47 | Signal transducer and activator of transcription 1 |
2q32.2 |
| ATF2 | 19.7 | 14.37±0.27 | Activating transcription factor | 2q32 |
| MYOD | 15.9 | 16.62±1.62 | myogenic differentiation 1 | 11p15.4 |
| SYBL1 | 13.2 | 18.56±5.24 | Synaptobrevin-like 1 | Xq28 Y28 |
| NPAT | 15.9 | 14.19±1.64 | Nuclear protein, ataxia- telangiectasia locus |
11q22-q23 |
| STAT5 | 22.5 | 15.68±5.05 | Signal transducer and activator of transcription 5A |
17q11.2 |
| CIITA | 16.3 | 9.36±0.87 | class 2 MHC transactivator | 16p13 |
| HOXA2 | 21.8 | 21.75±7.21 | Homeobox A2 | 7p14p15 |
| GATA3 | 6.4 | 15.11±0.57 | Gata binding protein | 10p15 |
| SIM2 | 7.6 | 15.87±1.55 | Single minded homologue 1 | 21q22.13 |
| WT1 | 10.2 | 17.46±2.08 | Wilms tumor1 | 11p13 |
| Cell Cycle genes | ||||
| p27KIP1 | 17.0 | 17.35±4.65 | Cyclin-dependent kinase inhibitor |
12p13.1-p12 |
| CDC2 | 12.9 | 10.65±2.69 | Cell division cycle 2 | 10q21.1 |
| CyclinD2 | 22. 4 | 16.33±1.19 | Cyclin D2 | 12p13 |
| CDKN2A | 6.2 | 17.56±4.25 | cdk inhibitor 2a | 9p21 |
| p21 | 11.8 | 17.70±2.90 | cyclin-dependent kinase inhibitor 1A |
6p21.2 |
| K-RAS | 21.6 | 16.89±2.84 | Kirsten rat sarcoma virus oncogene |
12p12.1 |
| TP73 | 11.1 | 14.99±3.84 | Tumor protein p73 | 1p36.3 |
| Apoptotic genes | ||||
| CASP8 | 6.4 | 34.18±4.37 | Caspase 8 | 2q33-q34 |
| CD14 | 11.4 | 35.51±3.79 | CD14 | 5q31.1 |
| Membrane proteins | ||||
| MDR1 | 6.2 | 13.66±0.56 | Multiple drug resistant 1 (p- glycoprotein) |
7q21.1 |
| MLC1 | 11.4 | 14.07±2.29 | Megalencephalic leukoencephalopathy with subcortical cysts 1 |
22q13.33 |
| CFTR | 10.9 | 8.45±1.90 | cystic fibrosis transmembrane conductance regulator |
7q13.2 |
| MTX | 14.4 | 16.49±3.97 | Metaxin | 1q21 |
| GPC3 | 5.7 | 17.89±3.72 | Glypican 3 | Xq26.1 |
| GLUT4 | 8.6 | 12.25±1.09 | Solute carrier insulin transport | 17p13 |
| Glucose Metabolism | ||||
| G6PD | 14.2 | 12.19±1.89 | Glucose-6-phosphate dehydrogenase |
Xq28 |
| DNA repair gene | ||||
| MGMT | 7.0 | 17.73±2.90 | O-6-methylguanine-DNA methyltransferase |
10q26 |
| Immune related | ||||
| IFN | 6.7 | 16.37±1.52 | Interferon | 9p22 |
| LAGE-1 | 22.98 | 14.53±2.00 | CTAG2/cancer/testis antigen 2 |
Xq28 |
| GAGE 1 | 17.2 | 17.51±3.16 | G antigen 1 | Xp11.4-11.2 |
| IL4 | 11.2 | 11.60±0.43 | Interleukin 4 | 5q31.1 |
| PDGF-B | 10.7 | 19.93±1.43 | Platelet-derived growth factor beta polypeptide |
22q13.1 |
| KIRDL4 | 8.7 | 12.08±3.31 | Killer cell immunoglobulin like receptor 2DL4 |
19q13.4 |
| Angiogenesis Inhibitors | ||||
| TIMP3 | 22.3 | 12.47±3.44 | Tissue inhibitor of metallopeptidases-3 |
22q12.3 |
| PAI-1 | 26.8 | 21.76±3.53 | Plasminogen activator inhibitor 1 |
7q21.3-q22 |
| TSP1 | 23.01 | 15.58±3.27 | Thrombospondin 1 | 15q15 |
| Other genes | ||||
| RIOK3 | 11.6 | 13.06±3.12 | RIO kinase 3, Serine threonine kinase activity, nucleotide binding |
18q11.2 |
| NIS | 13.3 | 13.32±0.34 | sodium-iodide symporter | 19p13.2-p12 |
| POMC | 20.5 | 19.89±1.57 | Proopiomelanocortin | 2p23.2 |