Value of Methylation Status of RPRM, SDC2, and TCF4 Genes in Plasma for Gastric Adenocarcinoma Screening

Figures & data

Figure 1 Hub gene screening and analysis. (A) Venn diagram (The 3 datasets showed an overlap of 197 genes). (B) *TCF4 were statistically significant.

Table 1 GO and KEGG Pathway Enrichment Analysis of DEGs in Stomach Cancer

Term	Description	Count	FDR
GO:0008284	Positive regulation of cell proliferation	39	4.25E-19
GO:0043410	Positive regulation of MAPK cascade	25	4.25E-19
GO:0007169	Transmembrane receptor protein tyrosine kinase signaling pathway	22	3.56E-17
GO:0033674	Positive regulation of kinase activity	17	3.91E-15
GO:0018108	Peptidyl-tyrosine phosphorylation	20	2.60E-14
GO:0005576	Extracellular region	68	8.70E-19
GO:0043235	Receptor complex	21	1.20E-12
GO:0005615	Extracellular space	52	9.99E-11
GO:0005886	Plasma membrane	89	6.51E-10
GO:0005887	Integral component of plasma membrane	41	2.53E-08
GO:0004714	Transmembrane receptor protein tyrosine kinase activity	22	1.50E-18
GO:0004713	Protein tyrosine kinase activity	15	6.73E-10
GO:0005125	Cytokine activity	18	6.73E-10
GO:0008083	Growth factor activity	16	7.17E-09
GO:0005102	Receptor binding	20	7.81E-07
hsa05200	Pathways in cancer	46	2.08E-18
hsa04151	PI3K-Akt signaling pathway	27	1.53E-08
hsa05205	Proteoglycans in cancer	17	1.57E-05
hsa04010	MAPK signaling pathway	20	1.78E-05

Abbreviations: GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; DEGs, differentially expressed genes; FDR, false discovery rate; MAPK, mitogen-activated protein kinase.

Figure 2 Pathological morphology. (A) gastric adenocarcinoma HE X200 (B) gastritis HE X200.

Table 2 Basic Characteristics of Patients and Controls

	GAC, N(%) N=61	Control, N(%) n=227	P value Χ^2 test
Sex			<0.001*
Male	52(85.2%)	114(50.2%)
Female	9(14.8%)	113(49.8%)
Age, years			<0.001*
≤60	24(39.3%)	174(76.7%)
>60	37(60.7%)	53(23.3%)

Note: *P<0.01.

Abbreviation: GAC, gastric adenocarcinoma.

Table 3 Results of Gastroscopy/Tissue Biopsy and Methylation of RPRM, SDC2, and TCF4 in Plasma

Gastroscopy/tissue biopsy	N	RPRM		SDC2		TCF4		Combined
		+	–	+	–	+	–	+	–
+	61	37	24	37	24	41	20	49	12
–	227	4	223	4	223	10	217	15	212
Total	288	41	247	41	247	51	237	64	224
χ^2		136.585		136.585		130.154		151.179
P value		<0.001*		<0.001*		<0.001*		<0.001*
Sensitivity		60.66%		60.66%		67.21%		80.33%
Specificity		98.24%		98.24%		95.59%		93.39%
Youden’s index (%)		58.89%		58.89%		62.81%		73.72%
PPV		0.902		0.902		0.804		0.766
NPV		0.903		0.903		0.916		0.946
Kappa score		0.669		0.669		0.668		0.724

Note: *P<0.01.

Abbreviations: RPRM, Reprimo; SDC2, Syndecan-2; TCF4, Transcription factor 4; PPV, positive predictive value; NPV, negative predictive value.

Figure 3 (A) methylation of RPRM, SDC2 and TCF4 were positive in GAC. (B) Internal reference ACTB express in gastritis.