Table 2.
Overview of differentially methylated genes in PDAC tissue. Compiled and modified from [41,52] and references therein.
| Gene Nature | Meth. Status 1 | Gene Names and Categories | ||
|---|---|---|---|---|
| Cancer Genes [52] 2 | ||||
| Tumor suppressor | + | UCHL1 (100%), MDF-1 * (96%), SPARC/ON (94%), PENK * (93%), RPRM (91%), mi-R9-1 * (89%), ADAMTS ** (88–90%), CCND (86%), SIP1 (73%), BNC1 (65–78%), PCDH10 (61%), SOCS-1 (57%), APC, RAR-β (56%), CDKN2A (33%), ATP4A, BMP3, BRCA1, CADM1, Cyclin D2, DNAJC15, FOSB, GSG1, KLF6, KLF10, miR-506, MLH1, PARP6, RASSF1A, ZPF82, ZNF415 | ||
| − | SERPINB5 (87%), CLDN4 (85%), LCN2 * (85%), SFN (85%), MUC4 2 (80%), TFF2 (65%), PSCA ** (30%), MAP4K4 **, SULT1E1 | |||
| +/− | CDKN1C (78%), FOXE1 (64%) | |||
| Oncogene | + | mi-R9-1 * (89%), ADAMTS ** (87.5–90%), KRAS (33%) | ||
| − | MUC4** (80%), S100P *** (57%), S100A4 (50%), PSCA ** (30%), IGF2BP3, MAP4K4 **, MSLN | |||
| Epigenetic regulatory genes [41] | ||||
| Writers | Readers | Erasers/editors | ||
| DNA methylation | + | DNMT3A | MBD1, ZMYM4 | IDH2, MGMT |
| − | DNMT1 | CHD2 | APOBEC1, TET3 | |
| +/− | DNMT3B | CHD7, ZBTB38, ZMYM6 | ||
| Histone methylation | + |
EHMT2, KMT2D, MECOM, PRDM8, PRDM12, PRDM13, PRDM14, SETBP1, SETD7, SETMAR, SMYD2, WHSC1L1 |
DNMT3A | KDM3A, KDM6B |
| − | EZH2, PRDM2, PRDM11, PRDM15, WHSC1 | ATXN7, CHD2, DHX30, EHMT2, GATAD2A, ZMYM8 | KDM2A, KDM2B, KDM3B, KDM4B | |
| +/− | EHMT1, KMT2C, PRDM1, PRDM4, PRDM6, PRDM7, PRDM16, SETD3, SMYD3 | CBX5, CHD7, EHMT1, UHRF1 | ||
| Histone acetylation | + | KAT2A | BRD4 | HDAC11 |
| − | GTF3C1, NCOA2, NCOA7 | ATXN7, BRD1, BRD3, DHX30, GATAD2A, ZMYM8 | HDAC5, HDAC9, SIRT6, SIRT7 | |
| +/− | CREBBP, KAT6B, NCOA1 | HDAC4 | ||
| Arginine methylation | + | PRMT6 | ||
| +/− | PRMT8 | |||
| Chromatin remodeler | + | SMARCA2 | ||
| − | CHD2, DPF3, SMARCD3, TTF2 | |||
| +/− | ARID1B, CHD7, CHD8 | |||
| Histone protein | + | HIST3H2BB, HIST2H2BF, HIST1H2BI, HIST1H3B, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H4F | ||
| − | H1F0, H1FOO, HIST1H1E, HIST1H2AG, HIST1H2APS1, HIST1H2BA, HIST1H2BC, HIST1H2BN, HIST1H3C, HIST1H3H, HIST1H4H | |||
| +/− | HIST3H2A | |||
| Developmental and signaling genes [41] | ||||
| Homeobox-containing genes | + | HHEX, HOPX, HOXA, HOXC HOXD, IRX2, IRX4 (68%), MSX, PPRX, SHOX2, SOX15, ZEB1 | ||
| − | TGIF1, TGIF2, ZEB1 | |||
| +/− | HOXB, PAX | |||
| Pancreatic development | + | FOXA1, GATA3, HLX, ISL1, MEIS2, NEUROG3, NKX2-2, NKX6- 1, PAX6 | ||
| − | HNF4A | |||
| +/− | HNF1B, MMP2, MMP9, MNX1, NKX6-2, ONECUT1, SOX9 | |||
| Pancreatic signaling | + | EGF, FGF10 | ||
| − | HGFAC | |||
| +/− | NOTCH1 | |||
| Other differentially methylated genes [41] | ||||
| Genes associated with patient survival patient survival |
n.a. | ATP4A, FOSB, GSG1, KLF6 | ||
1 Meth. = methylation status, + = hypermethylated, − = hypomethylated, n.a. = not available, 2 methylation frequencies in brackets, where available (source: [52]), * partial tumor suppressor, ** tumor suppressor or oncogene, dependend on tissue or cancer type, *** oncogene, might also have tumor suppressor function.