Table 2.
List of the 42 most differentially methylated genes (37 more methylated in hmMSI-H and 5 in SAC) as obtained from the array analysis
| Gene symbol | >methyl. in | adj p val. | Gene name | Chr |
|---|---|---|---|---|
| PDCD2L | hmMSI-H | 0.00101 | Programmed cell death 2-like | 19 |
| FGFR2 | SAC | 0.00147 | Fibroblast growth factor receptor 2 | 10 |
| CTSL2 | hmMSI-H | 0.00159 | Cathepsin L2 | 9 |
| TLR4 | hmMSI-H | 0.00159 | Toll-like receptor 4 | 9 |
| ANKRD10 | hmMSI-H | 0.00350 | Ankyrin repeat domain 10 | 13 |
| COPZ1 | hmMSI-H | 0.00420 | Coatomer protein complex, subunit zeta 1 | 12 |
| C17orf108 | SAC | 0.00420 | Chromosome 17 open reading frame 108 | 17 |
| CEP68 | hmMSI-H | 0.00580 | Centrosomal protein 68 kDa | 2 |
| ZNF652 | hmMSI-H | 0.00580 | Zinc finger protein 652 | 17 |
| PCYOX1L | hmMSI-H | 0.00583 | Prenylcysteine oxidase 1 like | 5 |
| GALNT11 | hmMSI-H | 0.00583 | UDP-NADG:polypeptide N-acetylgalactosaminyltransferase 11 | 7 |
| MICAL2 | hmMSI-H | 0.00583 | Microtubule-associated monoxygenase, calponin and LIM domain 2 | 11 |
| OSCP1 | hmMSI-H | 0.00583 | Organic solute carrier partner 1 | 1 |
| ACAD10 | hmMSI-H | 0.00583 | Acyl-CoA dehydrogenase family, member 10 | 12 |
| MELK | hmMSI-H | 0.00583 | Maternal embryonic leucine zipper kinase | 9 |
| HLA-DOA | hmMSI-H | 0.00583 | Major histocompatibility complex, class II, DO alpha | 6 |
| KRT20 | hmMSI-H | 0.00583 | Keratin 20 | 17 |
| TMEM45B | hmMSI-H | 0.00583 | Transmembrane protein 45B | 11 |
| LOC285401 | SAC | 0.00641 | Uncharacterized LOC285401 | 3 |
| PPIL1 | hmMSI-H | 0.00650 | Peptidylprolyl isomerase (cyclophilin)-like 1 | 6 |
| CA13 | hmMSI-H | 0.00709 | Carbonic anhydrase XIII | 8 |
| BCL7C | hmMSI-H | 0.00709 | B cell CLL/lymphoma 7C | 16 |
| CD14 | hmMSI-H | 0.00850 | CD14 molecule | 5 |
| PLA2G4C | hmMSI-H | 0.00905 | Phospholipase A2, group IVC (cytosolic, calcium-independent) | 19 |
| LY6G6D | hmMSI-H | 0.00908 | Lymphocyte antigen 6 complex, locus G6D | 6 |
| TCF7L2 | hmMSI-H | 0.00954 | Transcription factor 7-like 2 (T-cell specific, HMG-box) | 10 |
| RP11-165H20.1 | hmMSI-H | 0.00954 | CHIA-like pseudogene | 1 |
| CHD6 | hmMSI-H | 0.00954 | Chromodomain helicase DNA-binding protein 6 | 20 |
| PARN | hmMSI-H | 0.00954 | Poly(A)-specific ribonuclease | 16 |
| KCNK15 | hmMSI-H | 0.00954 | Potassium channel, subfamily K, member 15 | 20 |
| TMEM209 | hmMSI-H | 0.01015 | Transmembrane protein 209 | 7 |
| GOLM1 | hmMSI-H | 0.01016 | Golgi membrane protein 1 | 9 |
| ARRDC1 | hmMSI-H | 0.01016 | Arrestin domain containing 1 | 9 |
| TRIM21 | hmMSI-H | 0.01016 | Tripartite motif containing 21 | 11 |
| PHAX | hmMSI-H | 0.01016 | Phosphorylated adaptor for RNA export | 5 |
| NMT2 | hmMSI-H | 0.01016 | N-myristoyltransferase 2 | 10 |
| ATP12A | hmMSI-H | 0.01016 | ATPase, H+/K+ transporting, nongastric, alpha polypeptide | 13 |
| ARHGAP30 | SAC | 0.01016 | Rho GTPase-activating protein 30 | 1 |
| WWP1 | hmMSI-H | 0.01055 | WW domain-containing E3 ubiquitin protein ligase 1 | 8 |
| GNAI3 | hmMSI-H | 0.01055 | Guanine nucleotide binding (G protein), α inhibit polypeptide 3 | 1 |
| CD48 | SAC | 0.01055 | CD48 molecule | 1 |
| EXPH5 | hmMSI-H | 0.01070 | Exophilin 5 | 11 |
Genes chosen for validation by pyrosequencing, qPCR, and IHC are written in bold letters
SAC serrated adenocarcinoma, hmMSI-H colorectal carcinoma showing molecular and histological features of microsatellite instability