Metastatic suppressor genes inactivated by aberrant methylation in gastric cancer

Table 1 Adaptor used in MCA-RDA and their sequence

Adaptor	Sequence
RXMA24	5'-AGCACTCTCCAGCCTCTCACCGAC-3'
RXMA12	5'-CCGGGTCGGTGA-3'
JXMA24	5'-ACCGACGTCGACTATCCATGAACC-3'
JXMA12	5'-CCGGGGTTCATG -3'
NMCA24	5'-GTTAGCGGACACAGGGCGGGTCAC-3'
NMCA12	5'-CCGGGTGACCCG-3'

Table 2 MSP primers of gene PTPRG

Methylated primers	5'-GTTCGTTCGTTTTTTCGTTC-3'
	5'-CATACTCCTAAAAATTATAACTCCGAC-3'
Unmethylated primers	5'-TTTTGTTTGTTTGTTTTTTTGTTTG-3'
	5'-AATCCATACTCCTAAAAATTATAACTCCA-3'

Table 3 RT-PCR primers of PTPRG gene

PTPRG primer	5'-CTAATAAGGGATGTTCACATGAAGC-3'
	5'-CTGTATTTTAATGGAGTGGATAGCA-3'
β-actin primer	5'-AAATCGTGCGTGACATTAA-3'
	5'-CTCGTCATACTCCTGCTTG-3'

Table 4 Features of fragments with different methylation

Fragment	Length (bp)	GC %	CpG/GpC	Chromosome Positioning	Similarity rate %	S	E
KL2	198	55.0	0.5625	1q23.1	100	404	e-110
KL5	106	71.2	0.7142	15	100	222	e-56
KL6	159	59.4	1.0714	1p36.31-36.23	98	141	2e-31
KL8	194	61.1	0.8461	2q33.3	99	396	e-108
KL14	347	72.3	0.9811	4p15	100	585	e-165
KL19	258	58.3	0.7692	5p15.1	97	480	e-133
KL22	332	64.1	0.7027	3p21	99	527	e-147
KL23	287	70.7	1.0606	1q42.1-43	98	458	e-126
KL33	136	53.2	0.9629	2p24.3-24.1	100	129	6e-28
KL40	255	66.2	1.1428	4p16.1	99	404	e-110
KL55	268	65.6	0.7894	18	92	231	e-152
KL59	282	64.5	0.6471	9p21	100	571	e-160
KL68	251	62.5	0.6000	4	87	173	4e-39
KL71	213	69.9	0.8260	10p12.1	100	434	e-119
KL74	341	69.5	0.7317	9p21	99	668	0
KL79	225	61.3	0.4782	13q13	98	458	e-127
KL82	403	67.4	0.8043	8q21.2	99	383	e-104
KL87	275	51.9	1.0000	11	97	515	e-144
KL95	360	70.8	0.7608	Xp22.3	100	726	0

Table 5 Methylation and mRNA expression of gene PTPRG n (%)

Tissue	PTPRG gene methylation		PTPRG mRNA expression
	U	M
Primary tumor	28 (77.78)	9 (25.0)	18 (50.0)
Metastatic lymph nodes	23 (63.89)	19 (52.78)a	9 (25.0)a
Before cell line treatment	+	+	-
After cell line treatment	+	-	+

^aP < 0.05. U: Unmethylation; M: Methylation.

Table 6 The relationship between PTPRG methylation in metastatic lymph nodes and absent expression of mRNA.

PTPRG methylation	PTPRG mRNA expression (%)
	+	-
+	1 (5.26)	18 (94.73)
-	9 (52.94)	8 (47.05)

χ² = 10.17, P < 0.01.