Glycosylation-related gene expression in HT29-MTX-E12 cells upon infection by Helicobacter pylori

Table 1 Differentially expressed genes associated with Helicobacter pylori infection of E12 cells

Gene symbol	P-value	Fold change	Gene name
Top 15 upregulated
1CLIP1	0.0025	5.42	CAP-GLY domain containing linker protein 1
C10orf118	0.0031	5.21	chromosome 10 open reading frame 118
TOP1	0.0352	5.09	topoisomerase (DNA) I
LARS	0.0054	5.02	leucyl-tRNA synthetase
CDC27	0.0073	4.95	cell division cycle 27 homolog (S. cerevisiae)
STIP1	0.0042	3.92	stress-induced-phosphoprotein 1
MALAT1	0.0077	3.82	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)
IL32	0.0021	3.54	interleukin 32
SLC39A6	0.0204	3.33	solute carrier family 39 (zinc), member 6
AHNAK2	0.0070	3.25	AHNAK nucleoprotein 2
HSP90AB1	0.0014	3.24	heat shock protein 90 kDa alpha (cytosolic), B1
ACTR2	0.0035	3.20	ARP2 actin-related protein 2 homolog (yeast)
EIF4G1	0.0349	3.16	eukaryotic translation initiation factor 4 gamma, 1
ACBD3	0.0253	3.14	acyl-CoA binding domain containing 3
CCND1	0.0222	3.09	cyclin D1
Top 15 downregulated
PDK4	0.0011	3.25	pyruvate dehydrogenase kinase, isozyme 4
BCAT1	0.0042	3.24	branched chain amino-acid transaminase 1, cytosolic
PELI1	0.0059	3.24	Pellino homolog 1 (Drosophila)
CYP3A5	0.0015	3.12	cytochrome P450, family 3, subfamily A, polypeptide 5
HPGD	0.0032	3.10	hydroxyprostaglandin dehydrogenase 15-(NAD)
LRRC31	0.0030	3.05	leucine rich repeat containing 31
KIAA1984	0.0082	2.97	KIAA1984
HNRNPD	0.0054	2.86	Heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)
IL28A	0.0026	2.85	interleukin 28A (interferon, lambda 2)
DDX60	0.0026	2.84	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60
PHF14	0.0021	2.82	PHD finger protein 14
LOC100288092	0.0025	2.82	Hypothetical protein LOC100288092
ZNF207	0.0027	2.82	zinc finger protein 207
NCOA2	0.0025	2.81	nuclear receptor coactivator 2
AHSA2	0.0064	2.72	AHA1, activator of heat shock 90 kDa protein ATPase homolog 2 (yeast)

¹qRT-PCR analysis showed CLIP1 was downregulated.

Table 2 Glycosylation-related differentially expressed genes associated with Helicobacter pylori infection of E12 cells

Gene symbol	Fold change	P value	Gene name
Top 20 upregulated
LGALS7/7B	2.31	0.0115	Lectin, galactoside-binding, soluble, 7 /7B
UGGT1	1.98	0.0059	UDP-glucose glycoprotein glucosyltransferase 1
ST3GAL5	1.90	0.0035	ST3 beta-galactoside alpha-2,3-sialyltransferase 5
PARM1	1.87	0.0026	Prostate androgen-regulated mucin-like protein 1
NAGK	1.79	0.0016	N-acetylglucosamine kinase
VSIG1	1.71	0.0240	V-set and immunoglobulin domain containing 1
EDEM2	1.69	0.0032	ER degradation enhancer, mannosidase alpha-like 2
MPDU1	1.69	0.0029	Mannose-P-dolichol utilization defect 1
DPM2	1.61	0.0015	Dolichyl-phosphate mannosyltransferase polypeptide 2, reg. s/u
LMAN2	1.60	0.0021	Lectin, mannose-binding 2
GMPPB	1.59	0.0019	GDP-mannose pyrophosphorylase B
ALG3	1.59	0.0214	Asn-linked glycosylation 3, alpha-1,3- mannosyltransferase hom.
GALK2	1.57	0.0027	Galactokinase 2
DDOST	1.53	0.0094	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase
MCAM	1.53	0.0111	Melanoma cell adhesion molecule
B3GALT6	1.53	0.0097	UDP-Gal:betaGal beta 1,3-galactosyltransferase polypeptide 6
SLC35B1	1.51	0.0025	Solute carrier family 35, member B1
ST6GALNAC4	1.50	0.0024	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4
GMPPA	1.49	0.0031	GDP-mannose pyrophosphorylase A
ALDOC	1.48	0.0020	Aldolase C, fructose-bisphosphate
Top 20 downregulated
REG4	2.46	0.0018	Regenerating islet-derived family, member 4
OGT	2.25	0.0037	O-linked N-acetylglucosamine (GlcNAc) transferase (OGT)
AMIGO2	2.22	0.0039	Adhesion molecule with Ig-like domain 2
GALNT12	2.09	0.0033	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12
EXT1	1.99	0.0256	Exostosin 1
LY75	1.86	0.0075	Lymphocyte antigen 75 (CLEC13B)
PIGZ	1.82	0.0072	Phosphatidylinositol glycan anchor biosynthesis, class Z
UGP2	1.79	0.0320	UDP-glucose pyrophosphorylase 2
MANEA	1.79	0.0225	Mannosidase, endo-alpha
ALG13	1.78	0.0138	Asparagine-linked glycosylation 13 homolog (S. cerevisiae)
GBAP1	1.75	0.0035	Glucosidase, beta, acid pseudogene 1
SLC35A3	1.73	0.0071	Solute carrier family 35 (UDP-N-acetylglucosamine transporter), member A3
ST3GAL4	1.71	0.0032	ST3 beta-galactoside alpha-2,3-sialyltransferase 4
B4GALNT3	1.71	0.0129	Beta-1,4-N-acetyl-galactosaminyl transferase 3
HMMR	1.70	0.0039	Hyaluronan-mediated motility receptor (RHAMM)
B4GALT6	1.69	0.0134	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6
MAN2A1	1.60	0.0034	Mannosidase, alpha, class 2A, member 1
LGALS2	1.58	0.0127	Lectin, galactoside-binding, soluble, 2
MAN1A1	1.53	0.0021	Mannosidase, alpha, class 1A, member 1
MUC13	1.53	0.0038	Mucin 13, cell surface associated
CD164	1.52	0.0015	CD164 molecule, sialomucin
B4GALT5	1.51	0.0071	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5

Table 3 qRT-PCR significance of selected genes

Gene	Fold Change	Regulation	Significance
GNE	1.84	Down	1
MUC20	1.77	Down	1
REG4	3.06	Down	1
MAN2A2	1.76	Down	1
MAN2B2	1.91	Down	NS P < 0.1
SLC35A2	1.53	Down	NS P < 0.1
RHOA	1.35	Down	NS P < 0.1
1TFF1	10.37	Down	NS P < 0.2
MAN2A1	1.42	Down	NS P < 0.2
ST3GAL5	2.00	Down	NS P < 0.2
MUC13	3.66	Down	NS
PDK4	1.65	Down	NS
GALNT10	2.74	Down	NS
GALNT7	1.68	Down	NS
MGAT2	2.09	Down	NS
MUC1	1.66	Down	NS
NEU1	1.54	Up	NS
CLIP1	2.37	Down	NS
LGALS2	1.27	Up	NS
OGT	1.43	Down	NS
AMIGO2	1.14	-	NS
ALG8	1.15	-	NS
GALK2	1.14	-	NS
SLC35A3	1.23	Down	NS
FPGT	1.07	-	NS
CGN	1.26	Down	NS
TJP3	1.01	-	NS
OCLN	1.66	Down	NS
EPHA2	1.07	-	NS
IL32	1.00	-	NS
IL8	1.53	Up	NS

¹TFF1 is not shown in Figure 3, and four further genes (MGAT1, LGALS7, OSTC and LGALS7) are only shown in Supplementary Figure 2.