Identification of differential gene expressions in colorectal cancer and polyp by cDNA microarray

doi:10.3748/wjg.v18.i6.570

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Feb 14, 2012 (publication date) through Mar 7, 2025

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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. Feb 14, 2012; 18(6): 570-575
Published online Feb 14, 2012. doi: 10.3748/wjg.v18.i6.570

Table 1 Clinical characteristics of patients with colorectal cancer or polyps

Case	Sex	Age	Size in cm/n		Differentiation	Depth	Dukes
			CRC	CRP	CRC	Polyps
1	F	41	1.7/2	0.6/2	High	S	B1
2	M	37	0.9/1	1.2/3	Poor	Ss	C1
3	M	68	2.9/2	0.7/1	Poor	Sm	D1
4	F	27	2.8/1	1.4/1	Poor	Ss	C2
5	M	59	1.8/1	0.5/3	Moderate	S	C2
6	F	52	2.9/1	1.9/4	Poor	Ss	B2
7	M	71	3.3/2	0.4/1	High	Sm	B1
8	M	46	2.7/1	3.1/1	Moderate	Ss	C1
9	M	28	0.9/1	2.8/2	Poor	Sm	B1
10	F	36	2.6/1	0.4/1	Poor	Ss	C2
11	F	30	2.4/1	2.8/2	Moderate	S	C1
12	M	46	3.1/1	1.3/2	Poor	Sm	B1
13	M	62	1.5/1	2.0/3	Poor	Ss	C2
14	F	24	0.8/1	2.4/2	Moderate	Sm	C2
15	M	70	2.5/1	4.3/1	Poor	S	B2
16	M	43	3.2/2	3.7/1	High	Ss	B2

S: Serosa; Ss: Subserosa; Sm: Submucosa.

Table 2 Primers used for quantitative reverse transcription polymerase chain reaction analysis

Gene tag	Sequences	Tm (°C)	Cycle	Product (bp)
MTA1	5’-AGCCGTGCTTCGGTATCTT-3’	57	30	580
	5’-CCCGTTGTGCTGCTCGTA-3’
PDCD4	5′-GCTGAATTCGGATGGATGTAGAAAATGAGCAGA-3’	54	27	470
	5’-CTGCTCGAGTCAGTAGCTCTCTGGTTTAAGA-3’
TSC1	5′-ATCGCCTTTATGGAATGT-3’	49	29	510
	5’-GCTTGTGGTGGTTCAGTT-3’
PDGFRA	5’-ACCATAAGGCTCTTACTCT-3’	45	31	490
	5’-TTCTGGCACTTACCTACA-3’

Table 3 Identification of differential gene expression profile between colorectal cancer and adenomatous polyp lesions

Accession	Gene function	Gene tag	Ratio
AY421086	Programmed cell death 4	PDCD4	6.41 ± 0.10
AA630800	Interferon, γ-inducible protein 30	IFI30	1.31 ± 0.18
AA400973	Lipocalin 2 (oncogene 24p3)	LCN2	3.16 ± 0.22
AI817942	Zeta-chain associated protein kinase (70 kD)	ZAP70	3.29 ± 0.31
AA447515	Mad4 homolog	MAD4	2.35 ± 0.20
W47350	Retinoic acid receptor responder 3	RARRES3	0.18 ± 0.13
AA436401	TU3A protein	TU3A	5.40 ± 0.27
AI650283	Serum/glucocorticoid regulated kinase 2	SGK2	1.29 ± 0.13
NM003542	H4 histone family, member G	H4FG	7.04 ± 0.17
NM205510	Fibroblast growth factor receptor 1	FGFR1	2.94 ± 0.21
NM204434	Cyclin-dependent kinase inhibitor 2A	CDKN2A	3.16 ± 0.28
NM005438	FOS-like antigen-1	FOSL1	1.93 ± 0.25
NM005439	Myeloid leukemia factor 2	MLF2	2.17 ± 0.24
BC08072	v-raf murine sarcoma 3611 viral oncogene homolog 1	ARAF1	0.98 ± 0.15
NM020531	Chromosome 20open reading frame 3	C20ORF3	2.23 ± 0.21
NM033158	Hyaluronoglucosaminidase 2	HYAL2	4.16 ± 0.28
NM001950	E2F transcription factor 4,p107/p130-binding	E2F4	5.26 ± 0.28
BC059522	Ribosomal protein S30	FAU	2.58 ± 0.13
NM008583	Multiple endocrine neoplasia I	MEN1	3.89 ± 0.11
NM011492	Serine/threonine kinase 11	STK11	5.12 ± 0.27
NM133862	Fibrinogen, gamma polypeptide	FGG	3.0 4 ± 0.28
BC162533	GRO2 oncogene	GRO2	1.39 ± 0.30
NM000612	Insulin-like growth factor 2 receptor	IGF2	5.06 ± 0.29
NM005343	v-Ha-ras Harvey rat sarcoma viral oncogene homolog	HRAS	4.74 ± 0.27
NM002634	Prohibitin	PHB	2.98 ± 0.15
BC046375	p53-induced protein	PIG11	6.67 ± 0.29
NM004448	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	ERBB2	3.15 ± 0.17
NM010658	v-maf musculoaponeurotic fibrosarcoma oncogene family	MAFG	5.61 ± 0.04
NM022012	Mitogen-activated protein 3 kinase 11	MAP3K11	3.32 ± 0.06
NM023983	Melanoma adhesion molecule	MCAM	7.38 ± 0.14
NM014567	Breast cancer anti-estrogen resistance 1	BCAR1	5.12 ± 0.23
NM000535	Postmeiotic segregation increased 2	PMS2	5.17 ± 0.25
NM183243	Inosine monophosphate dehydrogenase 1	IMPDH1	7.14 ± 0.10
NM005380	Neuroblastoma, suppression of tumorigenicity 1	NBL1	5.62 ± 0.16
NM002429	Matrix metalloproteinase 19	MMP19	3.90 ± 0.22
NM002466	v-myb avian myeloblastosis viral oncogene homolog-like 2	MYBL2	9.70 ± 0.21
NM022588	Metastasis associated 1	MTA1	10.41 ± 0.37
NM017045	Retinoblastoma 1	RB1	2.81 ± 0.14
NC006104	SET translocation	SET	2.69 ± 0.11
NM002439	Phosphatase and tensin homolog	PTEN	3.94 ± 0.21
NM053455	Fibrinogen-like 2 GTPase activating	FGL2	3.40 ± 0.27
NM005638	ADP-ribosylation factor protein 1	ARFGAP	5.14 ± 0.25
NM032415	Mucosa associated lymphoid tissue lymphoma translocation gene 1	MALT1	4.84 ± 0.21
NM006283	Transforming acidic coiled-coil containing protein 1	TACC1	3.41 ± 0.13
NM00288	v-ral simian leukemia viral oncogene homolog B	RALB	4.12 ± 0.18
NM003766	Myosin-like BCL2-interacting protein	BECN1	5.05 ± 0.14
NG027821	TRK-fused gene	TFG	4.33 ± 0.28
NM005805	Cadherin 1,type 1,E-cadherin (epithelial)	CDH1	4.11 ± 0.26
NM001982	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	ERBB3	5.82 ± 0.15
NM133250	MutS (Escherichia coli) homolog 2	MSH2	2.13 ± 0.21
AY805747	Ras homolog gene family, member E	ARHE	3.61 ± 0.22
NM002884	RAP1A, member of RAS oncogene family	RAP1A	5.18 ± 0.27
NM000368	Tuberous sclerosis 1	TSC1	6.02 ± 0.14
L36953	Mothers against decapentaplegic homolog 4	MADH4	4.93 ± 0.26

Table 4 Differentially expressed genes between polyps and colorectal cancer

Accession	Gene function	Gene tag	Ratio
			A	B
AA191692	Stratifin	SFN	2.36 ± 0.25	3.86 ± 0.11^a
H15456	Calpain 1, (mu/I) large subunit	CAPN1	8.17 ± 0.20	10.25 ± 0.24^a
AA043501	v-maf musculoaponeurotic fibrosarcoma (avian) oncogene homolog	MAF	1.36 ± 0.08	4.85 ± 0.27^a
AA495936	Microsomal glutathione S-transferase 1	MGST1	-2.14 ± 0.23	2.90 ± 0.16^a
H23235	Platelet-derived growth factor receptor	PDGFRA	-0.15 ± 0.31	4.81 ± 0.14^a
AA430032	Pituitary tumor-transforming 1	PTTG	4.91 ± 0.23	11.46 ± 0.18^a
N94468	Jun B proto-oncogene	JUNB	1.27 ± 0.20	11.09 ± 0.14^a
T61948	FBJ murine osteosarcoma viral oncogene B homolog	FOSB	1.37 ± 0.31	10.21 ± 0.20^a

AA460168	Growth arrest and DNA damage inducible 34	GADD34	1.07 ± 0.15	4.15 ± 0.20^a
L36870	MAP kinase kinase 4	MKK4	4.01 ± 0.23	6.93 ± 0.24^a
AA426216	Malignant cell expression-enhanced gene	LENG4	7.03 ± 0.16	8.81 ± 0.23^a
AA486219	SRp25 nuclear protein	LOC51329	2.09 ± 0.12	6.18 ± 0.23^a
AA457705	Immediate early response 3	IER3	1.94 ± 0.25	9.17 ± 0.20^a
AA485377	v-fos FBJ murine osteosarcoma viral oncogene homolog	FOS	4.03 ± 0.27	7.21 ± 0.05^a
AA463204	Pleiomorphic adenoma gene-like 1	PLAGL1	7.11 ± 0.24	-4.16 ± 0.06^a
AA434373	E74-like factor 3 (epithelial-specific )	ELF3	1.09 ± 0.29	7.03 ± 0.15^a
AI677994	Fms-associated tyrosine kinase 3 ligand	FLT3LG	1.94 ± 0.32	4.35 ± 0.02^a
AA464600	v-myc avian myelocytomatosis viral oncogene homolog	MYC	3.27 ± 0.17	8.01 ± 0.13^a

^aP < 0.05. “-” indicates down-regulation. A: Polyps vs normal mucosae; B: Colorectal cancer vs normal mucosae.

Table 5 cDNA microarray data confirmed by quantitative reverse transcription-polymerase chain reaction

Gene function	Gene tag	Ratio
		cDNA microarray	qRT-PCR
Metastasis associated 1	MTA1	8.01 ± 0.47	6.72 ± 0.20^a
Programmed cell death 4	PDCD4	6.41 ± 0.10	5.35 ± 0.01^a
Tuberous sclerosis 1	TSC1	6.02 ± 0.14	4.83 ± 0.26^a
Platelet-derived growth factor receptor	PDGFRA	-0.15 ± 0.31	0.03 ± 0.07^a

^aP < 0.05. “-” indicates down-regulation.

Citation: Dai YC, Zhu XS, Nan QZ, Chen ZX, Xie JP, Fu YK, Lin YY, Lian QN, Sang QF, Zhan XJ. Identification of differential gene expressions in colorectal cancer and polyp by cDNA microarray. World J Gastroenterol 2012; 18(6): 570-575
URL: https://www.wjgnet.com/1007-9327/full/v18/i6/570.htm
DOI: https://dx.doi.org/10.3748/wjg.v18.i6.570