Table 1.
Differentially expressed enzymes and their function within the glycome. Enzymes affecting metabolism of glycolipids and glycoproteins whose expression levels change in response to HDAC inhibition are grouped according to their affected pathway and whether the protein product is associated with cancer (are in bold) or is the initial step in the biosynthetic pathway (are in italic). References documenting the gene product link to cancer indicated in parentheses
| Biosynthetic & other metabolic processes | ||
|---|---|---|
| Log2 Fold-change | Symbol | Gene Name |
| Multiple Pathways | ||
| −1.26 | FUT10 | α-(1,3)-fucosyltransferase 10 [46, 47] |
| −1.26 | FUT11 | α-(1,3)-fucosyltransferase 11 [46, 48, 49] |
| −1.56 | B4GALT2 | UDP-Gal:β-GlcNAc β-(1,4)-galactosyltransferase 2 [50] |
| 1.07 | B3GAT2 | β-(1,3)-glucuronyltransferase 2 |
| Glycoprotein | ||
| EGF Domain | ||
| −1.04 | POGLUT1 | Protein O-glucosyltransferase 1 [50–53] |
| 1.30 | LFNG | O-fucosylpeptide 3-β-GlcNAc transferase [50, 54] |
| N & O-Linked Pathways | ||
| 1.56 | B3GNT2 | N-acetyllactosaminide β-(1,3)-GlcNAc transferase 2 [50, 55] |
| Complex N-Linked Pathway | ||
| −1.10 | ALG13 | UDP-GlcNAc transferase subunit [50] |
| −1.09 | ALG10 | α-1,2-glucosyltransferase [56] |
| 5.16 | MAN1A1 | α-Mannosidase, class 1A, member 1 [8, 52] |
| 1.63 | MGAT4A | α-(1,3)-mannosyl-glycoprotein 4-β-N-acetylglucosaminyltransferase A [50, 56] |
| Complex O-linked Pathway | ||
| −1.28 | GALNT14 | Polypeptide GalNAc transferase 14 [8, 57, 58] |
| 1.00 | GALNT6 | Polypeptide GalNAc transferase 6 [8, 50] |
| −1.08 | GALNT7 | GalNAc transferase 7 [8, 50, 59, 60] |
| 1.79 | GCNT1 | β-(1,3)-galactosyl-O-glycosyl-glycoprotein β-1,6-GlcNAc transferase [50, 61, 62] |
| O-linked GAG synthesis | ||
| Core tetrasaccharide linker for HSPG, Chondroitin Sulfate, Dermatan sulfate | ||
| 2.85 | XYLT1 | Xylosyltransferase I [50, 63] |
| −1.36 | B3GALT6 | UDP-Gal:βGal β-(1,3)-Gal transferase polypeptide 6 (GALT2) |
| Chondroitin Sulfate | ||
| 1.85 | CGAT1 | Chondroitin sulfate N-acetylgalactosaminyltransferase 1 |
| HSPGs | ||
| 1.10 | EXT1 | Exostosin glycosyltransferase 1 [50] |
| −2.22 | NDST1 | N-deacetylase/N-sulfotransferase [50] |
| 1.30 | GLCE | Glucuronic acid epimerase [64, 65] |
| Glycolipid metabolism | ||
| 1.07 | KDEL1 | KDEL motif-containing protein 1 [50] |
| 1.07 | KDEL2 | KDEL motif-containing protein 2 [50] |
| Sphingolipid & Gangliosides (lactosylceramide modification) | ||
| 1.57 | A4GALT | α-(1,4)-galactosyltransferase [50] |
| 1.46 | ST3GAL5 | ST3 β-galactoside α-(2,3)-sialyltransferase 5 [50] |
| 2.80 | ST8SIA1 | ST8 (α-N-acetyl-neuraminide α-(2,8) sialyltransferase 1) |
| 1.30 | ST6GALNAC3 | ST6 (α-N-acetyl-neuraminyl-2,3-β-galactosyl-1,3) |
| GPI Anchor synthesis | ||
| 1.10 | PIGH | Phosphatidylinositol GlcNAc transferase subunit H [50] |
| −1.67 | PIGW | Phosphatidylinositol-glycan biosynthesis class W protein |
| −1.21 | PIGO | GPI ethanolamine phosphate transferase 3 [50] |
| −1.13 | PIGU | Phosphatidylinositol glycan anchor biosynthesis class U protein [50] |
| Polysialic acid | ||
| 2.71 | ST6GAL2 / SIAT2 | ST6 β-galactosamide α-2,6-sialyltranferase 2 |
| 1.27 | ST8SIA4 / SIA8D | ST8 α-N-acetyl-neuraminide α-2,8-sialyltransferase 4 [50] |
| Sulfation levels | ||
| General enzymes | ||
| 1.11 | PAPSS1 | 3′-phosphoadenosine 5′-phosphosulfate synthase 1 [50] |
| −1.09 | CHST10 | carbohydrate sulfotransferase 10 [50] |
| Sulfatases (HSPG) | ||
| 2.94 | SULF1 | Sulfatase 1 [66, 67] |
| 1.11 | SULF2 | Sulfatase 2 [66–68] |
| Protein sulfotransferase | ||
| 1.00 | TPST2 | Tyrosylprotein sulfotransferase 2 [50] |
| Lipid sulfotransferases - sphingolipid/ceramide | ||
| 1.38 | GAL3ST1 | Galactose-3-O-sulfotransferase 1 [69, 70] |
| N&O linked sulfotransferases | ||
| 1.35 | CHST8 | Carbohydrate (N-acetylgalactosamine 4–0) sulfotransferase 8 |
| −1.67 | CHST9 | Carbohydrate (N-acetylgalactosamine 4–0) sulfotransferase 9 [71–73] |
| Chondroitin / Dermatan sulfate | ||
| 1.25 | CHST11 | Carbohydrate (chondroitin 4) sulfotransferase 11 (C4ST-1) [50] |
| 1.05 | CHST12 | Carbohydrate (chondroitin 4) sulfotransferase 12 [50] |
| − 1.42 | CHST14 | Carbohydrate (dermatan 4) sulfotransferase 14 |
| 2.58 | GAL3ST4 | Galactose-3-O-sulfotransferase 4 [50] |
| Catabolic enzymes | ||
| Lysomal enzymes | ||
| 1.39 | NEU1 | Neuraminidase 1 (lysosomal sialidase) |
| 2.80 | FUCA1 | Fucosidase, α-L- 1, tissue [52] |
| Glycoprotein Unibiquitin ligases (ERAD pathway) | ||
| 1.03 | FBXO2 | F-box only protein 2 [50] |
| −3.01 | FBXO6 | F-box only protein 6 [50] |
| −1.66 | FBXO17 | F-box only protein 17 [50] |
| Metabolic enzymes | ||
| 1.67 | GALM | Galactose mutarotase [50] |