Comparative genomic study of gastric epithelial cells co-cultured with Helicobacter pylori

doi:10.3748/wjg.v18.i48.7212

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World Journal of Gastroenterology

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1007-9327

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

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World J Gastroenterol. Dec 28, 2012; 18(48): 7212-7224
Published online Dec 28, 2012. doi: 10.3748/wjg.v18.i48.7212

Table 1 Primer pairs for quantitative real-time polymerase chain reaction

Gene	Primer Sequence (5’ to 3’)		Size of PCR product (bp)
	Sense	Anti-sense
HDAC6	ACCGCTACGAGCAGGGTA	CGAGACGTGCAGGAAAGC	155
TARF1	TCCCGTAACACCTGATTAA	ACAACTCCCAAACCATACAC	146
GAPDH	AACGGATTTGGTCGTATTGGG	TCGCTCCTGGAAGATGGTGAT	216

PCR: Polymerase chain reaction.

Table 2 Pathological outcomes of gastric mucosae from Mongolian gerbils lavaged with the most virulent gastric carcinoma-derived strain, the least virulent chronic gastritis-derived strain, and the control broth over 52 wk

	Pathological outcomes
	Chronic gastritis	Gastric atrophy	Intestinal metaplasia	Gastric dysplasia	Gastric carcinoma
GC (n = 10)	9 (90.0%)^b	8 (80.0%)^b^d	8 (80.0%)^b^d	9 (90.0%)^b^d	6 (60.0%)^b^d
CG (n = 10)	9 (90.0%)^b	0 (0.0%)	0 (0.0%)	0 (0.0%)	0 (0.0%)
Control (n = 10)	0 (0.0%)	0 (0.0%)	0 (0.0%)	0 (0.0%)	0 (0.0%)

^bP < 0.01 vs control group;

^dP < 0.01 vs CG group. GC: Gastric carcinoma; CG: Chronic gastritis.

Table 3 Differentially expressed genes with a fold change of > 2.0 or < 0.5 in GES-1 cells co-cultured with the most virulent gastric carcinoma-derived strain vs the least virulent chronic gastritis-derived strain

Gene name (n = 185)	Fold change GC/CG	Accession number
Cell cycle related genes
AMN1	4.748	BG031897
HDAC6	2.025	NM_006044
CCNE2	0.464	AF112857
KIF20B	0.462	NM_016195
DOCK8	0.456	AL161725
ASPM	0.452	AK001380
CENPF	0.450	U30872
NIPBL	0.432	NM_015384
SYCP2	0.424	NM_014258
ASPM	0.414	NM_018123
SGOL2	0.401	N31731
CENPE	0.398	NM_001813
CEP70	0.382	NM_024491
SGOL2	0.375	AW965339
DOCK11	0.363	AI742838
SERPINB3	0.290	BC005224
Apoptosis-related genes
TRAF1	2.254	NM_005658
TIA1	0.496	AL567227
OPA1	0.474	AB011139
PIK3CA	0.450	NM_006218
NUDT12	0.408	AL136592
PEG10	0.367	BE858180
Cytoskeleton and sports
ADD3	0.450	AI818488
KIAA0774	0.429	AI818409
KIF14	0.379	AW183154
KIF14	0.370	NM_014875
ADD3	0.344	BE545756
ADD3	0.316	NM_019903
Intracellular transport
VPS13A	0.435	AW629014
VPS13A	0.438	AW629014
IFT74	0.431	NM_025103
GOLGA4	0.425	NM_002078
ANKRD10	0.419	BE670056
IFT80	0.414	AB037795
FAM8A1	0.412	NM_016255
SNX2	0.406	NM_003100
ANKRD32	0.355	AL136560
DNA synthesis, repair, recombination
RAD50	0.472	NM_005732
SFPQ	0.457	AV705803
FAM8A1	0.412	NM_016255
LIN9	0.338	BF697734
DNA-binding ,transcription, transcription factor
ZNF253	5.254	NM_021047
KLF11	3.598	AA149594
SMARCA1	0.496	NM_003069
GOLGB1	0.492	NM_004487
KLF9	0.462	NM_001206
CHD1	0.459	NM_001270
PBX1	0.455	AL049381
TRIP11	0.434	AF007217
SMARCA1	0.433	NM_003069
C8orf83	0.433	BE962119
EPM2AIP1	0.430	BF432224
ELL2	0.420	AI745624
GLCCI1	0.400	AA058770
ARID5B	0.395	BG285011
ZNF644	0.390	NM_016620
BAZ2B	0.365	NM_013450
SAMD9	0.352	AA741307
SAMD9	0.345	NM_017654
TPR	0.346	BF110993
TPR	0.344	AK023111
LCORL	0.339	AI807408
TPR	0.300	AW235355
Cell signal and transduction
PRKCB	0.498	M13975
DST	0.493	NM_001723
FARP1	0.462	BF725250
GMFB	0.461	NM_004124
PPM1A	0.454	AA886888
IFT81	0.444	NM_014055
PDE10A	0.442	AI143879
ICK	0.428	NM_014920
ANKRD10	0.419	BE670056
IFT80	0.414	AB037795
SNX2	0.406	NM_003100
CNTLN	0.386	AA280904
MAP2K6	0.384	NM_002758
ANKRD32	0.355	AL136560
ARHGAP18	0.307	BE644830
Protein translation, synthesis, decomposition
RHOBTB3	0.500	NM_014899
ST13	0.490	U17714
EEF2K	0.488	W68180
TSHZ2	0.476	AW953679
TMF1	0.417	AI767750
HMMR	0.410	U29343
CCDC88A	0.387	AB033038
NSBP1	0.321	BC005342
Protein-coding gene
CXorf39	0.499	AI590719
LOC286052	0.478	AA278233
FLJ40113/LOC440295	0.411	AI632181
LOC100133781	0.374	AA973100
LOC100130360	0.346	BG231554
LOC643401	0.300	BC039509
Ion channel and transport
IFT74	0.496	AI610355
SLC5A3	0.493	AK024896
SLC2A13	0.489	AL565362
STEAP4	0.488	NM_024636
TMEM56	0.469	AI004375
EXOC5	0.466	BF509391
CACNB2	0.465	AI040163
SLC2A13	0.455	NM_052885
TMEM133	0.435	AF247167
DMXL2	0.405	AB020663
SNX13	0.401	R75838
SEC62	0.397	NM_153039
ATP11C	0.382	BF475862
TMEM106B	0.380	BF513060
PEG10	0.367	BE858180
SORBS2	0.222	AI659533
Cell proliferation, angiogenesis
ANGPTL4	2.460	NM_016109
TPR	0.492	NM_003292
TPR	0.492	NM_003292
PNN	0.487	U59479
PNN	0.428	U59479
ROCK2	0.404	AL049383
TTK	0.347	NM_003318
Immune-related genes
CFI	0.477	NM_000204
SERPINB4	0.431	AB046400
PIBF1	0.423	NM_006346
Metabolize-related genes
AK7	0.477	NM_152327
TTC3	0.471	AI652848
HS2ST1	0.438	NM_012262
MANEA	0.427	AI587307
PLA2G12A	0.416	AV714268
TTC3	0.413	D83077
PPP1CB	0.407	W67887
NUDT12	0.408	AL136592
TTC3	0.403	NM_003316
TTC3	0.403	AI885338
RNF150	0.398	AA722069
SEPP1	0.396	NM_005410
CRYZ	0.387	NM_001889
PDK4	0.374	AV707102
ABAT	0.359	AF237813
PLA2G12A	0.331	AI767751
AGXT2L1	0.326	NM_031279
CYP1B1t	0.314	NM_000104
METTL7A	0.274	NM_014033
Cell structure-related genes
ARMCX3	0.385	AL121883
ANK3	0.225	NM_020987
Cell Adhesion-related genes
KITLG	0.447	AI446414
PIK3CA	0.450	NM_006218
ANKRD10	0.419	BE670056
ANKRD32	0.355	AL136560
Stress-related genes
DNAJB4	0.400	BG252490
LXN	0.294	NM_020169
DNAJB4	0.471	NM_007034
Protein regulation
LOC727770	0.426	AI359676
TBC1D8B	0.368	AW172431
Cell differentiation
LIFR	0.374	AA701657
RNA processing
SR140	0.413	AU152088
Protein receptor
LANCL1	0.412	NM_006055
Oxidation
DIO2	0.434	AI038059
Cell growth-related genes
ITCH	0.441	AA868238
TGFBR3	0.450	AW193698
TGFBR3	0.422	NM_003243
Cytokine receptor
LTB	2.001	NM_002341

Table 4 Most differentially expressed genes in GES-1 cells co-cultured with the most virulent gastric carcinoma-derived strain vs the least virulent chronic gastritis-derived strain

Gene name	Betweenness centrality	Description	Identified or proposed function
JUN	0.201780	Jun oncogene	Cell growth and/or maintenance, signal transduction molecules, and transcription factors
KRAS	0.185944	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	Regulation of cell cycle, cell growth and/or maintenance
BRCA1	0.162070	Breast cancer 1, early onset	DNA damage checkpoint; p53/ATM signaling, and induction of apoptosis
SMAD2	0.121460	SMAD family member 2	Transcription factors
TRAF1	0.092496	Tumor necrosis factor receptor-associated factor 1	DNA damage checkpoint, p53/NF-KB signaling, and cell cycle control
HDAC6	0.092239	Histone deacetylase 6	Cell proliferation and tumor angiogenesis

Citation: Wang F, Luo LD, Pan JH, Huang LH, Lv HW, Guo Q, Xu CX, Shen SR. Comparative genomic study of gastric epithelial cells co-cultured with Helicobacter pylori. World J Gastroenterol 2012; 18(48): 7212-7224
URL: https://www.wjgnet.com/1007-9327/full/v18/i48/7212.htm
DOI: https://dx.doi.org/10.3748/wjg.v18.i48.7212