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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]