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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

From: Alterations in the glycome after HDAC inhibition impact oncogenic potential in epigenetically plastic SW13 cells

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 [50,51,52,53]
 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 [66,67,68]
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 [71,72,73]
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]