Gene expression profiling reveals sequential changes in gastric tubular adenoma and carcinoma in situ

Table 1 Amplification efficiency of formalin-fixed tissues.

Sample	AmplificationMethod	Starting materials		Amplified RNA(ng)	3Amplification Fold (X)
		Total RNA (ng) (1mRNA)	2Cell number
Fresh MKN45			690	152.2	761 X
	4T7 IVT only	20 (0.2)
SNU484			650	213.2	1066 X
Fixed MKN45			830	121.6	608 X
	T7 IVT only	20 (0.2)
SNU484			1090	128.6	643 X
MKN45			830	42120	210600 X
	5PCR-T7 IVT	20 (0.2)
SNU484			1090	45016	225080 X

RNAs from fresh and formalin-fixed xenograft tumors of MKN45 and SNU484 cells were amplified under the same conditions as described in the Materials and Methods.

¹mRNA : estimated to be 1/100 of total RNA (ng). ²Cell number: estimated number of cells from tissue sections required to obtain the starting RNA (20ng). ³Amplification folds: aRNA/estimated starting mRNA.

⁴T7 IVT: in vitro transcription using T7 RNA polymerase.

⁵PCR-T7 IVT: 20 cycles of PCR followed by T7 IVT.

Table 2 Up-regulated genes.

Symbol	Annotation	GenBank
NUP153	Nucleoporin 153ku	NM_005124
CENPA	Centromere protein A (17 ku)	NM_001809
RPL23	Ribosomal protein L23	NM_000978
LMAN2	Lectin, mannose-binding 2	NM_006816
KIAA0469	KIAA0469 gene product	NM_014851
POLR2C	Polymerase (RNA) II (DNA directed) polypeptide C, 33 ku	NM_002694
G2AN	Alpha glucosidase II alpha subunit	NM_014610
KIAA0007	KIAA0007 protein	D26488
EPHB4	EphB4	NM_004444
YWHAQ	Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide	NM_006826
DHX9	DEAH (Asp-Glu-Ala-His) box polypeptide 9	NM_001357
K-ALPHA-1	Tubulin, alpha, ubiquitous	NM_006082
CPR2	Cell cycle progression 2 protein	NM_030900
PICALM	Phosphatidylinositol binding clathrin assembly protein	NM_007166
CXCL5	Chemokine (C-X-C motif) ligand 5	NM_002994
MGC3103	KUGI seq X - hypothetical protein MGC3103	NM_024036
CHUK	Conserved helix-loop-helix ubiquitous kinase	NM_001278
FLJ20297	Hypothetical protein FLJ20297	NM_017751
RPL4	Ribosomal protein L4	NM_000968
TFPI	Tissue factor pathway inhibitor (lipoprotein-associated coagulationinhibitor)	NM_006287
CD9	CD9 antigen (p24): tetraspanin superfamily	NM_001769
ZFP276	Zinc finger protein 276	NM_152287
HYOU1	Hypoxia up-regulated 1	NM_006389
HTATIP	HIV-1 Tat interactive protein, 60 ku	NM_006388
TMPO	Thymopoietin	NM_003276
FLJ10521	Hypothetical protein FLJ10521	NM_018125
GBAS	Glioblastoma amplified sequence	NM_001483
LOC51142	16.7 ku protein	NM_016139
LGTN	Ligatin	NM_006893
NEDD5	Neural precursor cell expressed, developmentally down-regulated 5	NM_004404
PAFAH1B2	Platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30 ku	NM_002572
RPIA	Ribose 5-phosphate isomerase A (ribose 5-phosphate epimerase)	NM_144563
ARHGEF9	Cdc42 guanine nucleotide exchange	NM_015185
RNPS1	RNA binding protein S1, serine-rich domain	NM_006711
RPL27	Ribosomal protein L27	NM_000988
RAMP	RA-regulated nuclear matrix-associated protein	NM_016448
PRKAG1	Protein kinase, AMP-activated, gamma 1 non-catalytic subunit	NM_002733
HMGB1	High-mobility group box 1	NM_002128
TOP1MT	Mitochondrial topoisomerase I	NM_052963
HNRPA0	Heterogeneous nuclear ribonucleoproteinA0	NM_006805
TRA1	Tumor rejection antigen (gp96) 1	NM_003299
BAP1	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	NM_004656
SMARCD2	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	NM_003077
FLJ11749	Hypothetical protein FLJ11749	NM_024591
RPL37	Ribosomal protein L37	NM_000997
RPS17	Ribosomal protein S17	NM_001021
HNRPM	Heterogeneous nuclear ribonucleoprotein M	NM_005968
AP3B1	Adaptor-related protein complex 3, beta 1 subunit	NM_003664
CRR9	Cisplatin resistance related protein CRR9p	NM_030782
KIAA0152	KIAA0152 gene product	NM_014730

Table 3 Down-regulated genes.

TFF2	Trefoil factor 2 (spasmolytic protein 1)	NM_005423
GALIG	Galectin-3 internal gene	NM_194327
TSPAN-1	Tetraspan 1	NM_005727
MUC5AC	Mucin 5, subtypes A and C, tracheobronchial/gastric	AJ001403
REG-IV	Regenerating islet-derived family, member 4	NM_032044
LOC376711	Similar to calpain 8	XM_352343
SYTL2	Synaptotagmin-like2	NM_032943
MT2A	Metallothionein2A	NM_005953
RPL13A	Ribosomal protein L13a	NM_012423
DPCR1	Diffuse panbronchiolitis critical region	NM_080870
IGL@	Immunoglobulin lambda locus	BM918733
TFF1	Trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in)	NM_003225
GUK1	Guanylate kinase 1	NM_000858
SLC25A19	Solute carrier family 25 (mitochondrial deoxynucleotide carrier), member 19	NM_021734
LGALS3	Lectin, galactoside-binding, soluble, 3	NM_002306
PSCA	Prostate stem cell antigen	NM_005672
FLJ38641	FLJ38641	AL358512
TSPAN-3	Tetraspan 3	NM_005724
KCNE3	Potassium voltage-gated channel, Isk-related family, member 3	NM_005472
GDDR	Down-regulated in gastric cancerGDDR	NM_182536
SERPINH1	Serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	NM_001235
ZNF265	Zinc finger protein 265	NM_005455
CYP2S1	Cytochrome P450, family 2, subfamily S, polypeptide 1	NM_030622
AGR2	Anterior gradient 2 (Xenepus laevis) homolog	NM_006408