Role of bacterial and genetic factors in gastric cancer in Costa Rica

Table 1 PCR primers for amplification of cagA, vacA and babA2 genes

Region	Primer	Nucleotide sequence	Reference
cagA	D008	5’-ATAATGCTAAATTAGACAACTTGAGCGA-3’	[28]
	R008	5’-TTAGAATAATCAACAAACATCACGCCAT-3’
	cagAFnz3	5’-AAAAGCGACCTTGAAAATTCC-3’	[29]
	cagA-seqR1	5’-TAGCATAATTGTCCAATTTCGC-3’
vacA s1	VA1-F	5’-ATGGAAATACAACAAACACAC-3’	[30]
	VA1-R	5’-CTGCTTGAATGCGCCAAAC-3’
vacA s1a	S1A-F1	5’-TCTYGCTTTAGTAGGAGC-3’	[30]
vacA s1b	SS3-F1	5’-AGCGCCATACCGCAAGAG-3’	[30]
vacA s1c	S1C-F1	5’-CTYGCTTTAGTRGGGYTA-3’	[13]
vacA s2	VA1-F1	5’-ATGGAAATACAACAAACACAC-3’	[30]
vacA m1	VA3-F	5’-GGTCAAAATGCGGTCATGG-3’	[30]
	VA3-R	5’-CCATTGGTACCTGTAGAAAC-3’
vacA m2	VA4-F	5’-GGAGCCCCAGGAAACATTG-3’	[30]
	VA4-R	5’-CATAACTAGCGCCTTGCAC-3’
babA2	babA-F	5’-AATCCAAAAAGGAGAAAAAGTATGAAA-3’	[31]
	babA-R	5’-TGTTAG TGATTTCGGTGTAGGACA-3’
	babA2-Fnc1	5’-GAAAAAACATGAAAAAACACATCCTTTCAT-3’
This study
	babA2-Rmn2	5’-TCTGGGTTAATGGCTTGCC-3’

¹Used with primer VA1-F.

Table 2 Characteristics of H pylori-positive Costa Rican patients

	Group A	Group B	P-value
Number of patients	101	90
Gender (male/female)	49/52	33/57	0.81
Mean age (yr, ± SD)	50.4 ± 11.5	50.9 ± 13.6	0.99
AG-positive (%)	36 (35.6)	24 (26.7)	0.12
IM-positive (%)	17 (16.3)	6 (6.7)	0.02

Table 3 Statistical analysis for several cytokine gene polymorphisms according to high gastric cancer incidence rate and gastric cancer in H pylori-positive Costa Rican patients

	High GCIR			Gastric cancer
	Pos/Neg	OR (95% CI)	P-value	Pos/Neg	OR (95% CI)	P-value
Interleukin-1&bgr;-511
T/T	28/19	1.9 (0.8-4.3)	0.136	18/47	1.6 (0.7-4.1)	0.283
T/C	50/43	1.4 (0.7-2.8)	0.317	24/93	1.2 (0.5-2.9)	0.629
C/C	23/28	1.0 reference		10/51	1.0 reference
Interleukin-1&bgr;+3954
T/T	2/0	-	-	-	0/2	-
T/C	56/45	1.4 (0.8-2.6)	0.237	39/101	2.1 (1.0-4.3)	0.049
C/C	43/45	1.0 reference		13/88	1.0 reference
Interleukin-1RN intron 2
*2/*2	20/11	2.2 (0.9-5.2)	0.078	4/31	0.7 (0.2-2.2)	0.494
*2/L	31/28	1.2 (0.6-2.3)	0.592	33/59	3.5 (1.7-7.3)	0.001
L/L	50/51	1.0 reference		15/101	1.0 reference
Interleukin-10-1082
A/A	52/49	1.3 (0.3-6.1)	0.766	35/101	3.2 (0.3-30.2)	0.304
G/A	46/37	1.6 (0.3-7.8)	0.551	16/83	1.8 (0.2-17.1)	0.617
G/G	3/4	1.0 reference		1/7	1.0 reference
Interleukin-10-592
A/A	11/12	0.7 (0.3-1.7)	0.406	10/23	3.1 (1.2-8.2)	0.022
C/A	34/31	0.9 (0.5-1.6)	0.668	26/65	3.2 (1.5-6.8)	0.002
C/C	56/47	1.0 reference		16/103	1.0 reference

-: Unable to compute. Pos: Positive; Neg: Negative.

Table 4 Patients with discordant H pylori vacA and babA2 genes from antrum and corpus biopsy specimens in the same stomach

Patient	Gene	Antrum	Corpus	Diagnosis	GCIR group
1	vacA	s2/m1	s1b/m1	AG	A (High GCIR)
2		s1b/m1	s2/m2	NAG	A
3		s1b/m1	s2/m2	AG	A
4		s1b/m1	s2/m2	AG + IM	A
5		s1b/m1	s1b/m2	AG + IMA	A
6		s1b/m1	s2/m2	AG	A
7		s1b/m1	s1b/m2	AG + IM	B (Low GCIR)
8	babA2	Pos	Neg	NAG	A
9		Neg	Pos	AG + IM	A

Table 5 Statistical analysis for the prevalence of H pylori genes or alleles in Costa Rican clinical isolates from groups A and B

Gene/allele	Group A (n = 41, %)	Group B (n = 35, %)	OR (95% CI)	P-value
cagA	36 (87.8)	23 (65.7)	3.9 (1.2-12.9)	0.026
vacA s1b	36 (87.8)	24 (68.6)	3.6 (1.1-12.1)	0.041
vacA m1	33 (80.5)	22 (62.9)	2.7 (0.9-8.0)	0.068
babA2	19 (46.3)	15 (42.9)	1.1 (0.4-2.8)	0.812

Table 6 Adjusted odd ratios with 95% confidence intervals and P-value for combinations of host and bacterial factors according to gastric cancer in Costa Rican H pylori-positive patients

Combination of factors	Gastric Cancer
	Pos/Neg	OR (95% CI)	P-value
IL-1&bgr;+3954_T/C, IL-1RN*2/L, IL-10-592_C/A
Pos	10/8	4.7 (1.7-13.0)	0.002
Neg	42/183
IL-1&bgr;+3954_T/C, IL-1RN*2/L, IL-10-592_C/A, vacA s1b/m1
Pos	9/2	7.2 (1.4-36.4)	0.017
Neg	40/74
IL-1&bgr;+3954_T/C, IL-1RN*2/L, vacA s1b/m1
Pos	18/4	9.8 (2.9-32.9)	< 0.001
Neg	31/72
IL-1RN*2/L, IL-10-592_C/A, vacA s1b/m1
Pos	14/9	3.0 (1.1-8.1)	0.028
Neg	35/67
IL-1&bgr;+3954_T/C, IL-10-592_C/A, vacA s1b/m1
Pos	21/9	4.7 (1.9-11.9)	0.001
Neg	28/67