Gene expression profiling: Canonical molecular changes and clinicopathological features in sporadic colorectal cancers

Table 1 Clinicopathological features relative to location of sporadic colorectal cancers

Clinicopathologic features	Tumor location1 (No. of patients)			P
	R (n = 27)	L (n = 29)	P (n = 28)
Male/Female	18/9	15/14	20/8	0.273
Age	62 ± 7	60 ± 12	62 ± 10	0.646
AJCC stage2, I/II/III/IV	4/13/6/4	4/15/6/4	4/10/9/5	0.926
Tumor differentiation, WD	22/5	29/0	24/4	0.021 (R vs L)
+ MD/PD + muc				0.052 (L vs P)
Synchronous adenoma, -/+	18/9	23/6	14/14	0.052 (L vs P)
LVN invasion, -/+	15/12	22/7	20/8	0.236

¹R: Cecum-splenic flexure of transverse colon; L: Splenic flexure of transverse colon-sigmoid colon; P: Rectum.

²According to the American Joint Committee on Cancer (6th ed., 2001). WD, MD, PD, and muc, well-, moderately-, poorly-differentiated, and mucinous. LVN: Lymphovascular or neural invasion of tumor cells.

Table 2 Number of differentially expressed genes in terms of molecular changes and clinicopathological features

Parameters	No. of patients (missing)	No. of differentiallyexpressed genes (P < 0.01), total (up/down)
Molecular changes1, -/+
APC mutations	55/27 (2)	83 (41/42)
Wnt-activated	45/38 (1)	82 (37/45)
MMR defects	70/14	238 (122/116)
RAF-mediated	58/26	108 (59/49)
Altered p53 expression	24/59 (1)	125 (57/68)
Crossover	64/19 (1)	92 (44/48)
Clinicopathologic features
Tumor location2, R/L + P	27/57	1628 (936/692)
R/L/P	27/29/28	1263
AJCC stage3, I + II/III + IV	50/34	195 (103/92)
Tumor differentiation, WD + MD/PD + muc	75/9	151 (69/82)
Synchronous adenoma, -/+	55/29	152 (92/60)
LVN invasion, -/+	57/27	279 (147/132)

¹Wnt-activated: explored by β-catenin assay, AXIN2 measurement, and GSK-3β immune staining; MMR defect: analyzed by MSI assay, MLH1 5'-promoter measurement or 3'-methylation, and MLH1 or MSH2 immune staining; RAF-mediated alterations: assayed by detection of mutations in BRAF V600E and KRAS exons 12 and 13, and MEK immune staining; Crossover: When a tumor carried both APC/Wnt-mediated alterations and MMR defects or RAF-mediated alterations.

²R: Caecum-splenic flexure of transverse colon; L: Splenic flexure of transverse colon-sigmoid colon; P: Rectum.

³According to the American Joint Committee on Cancer (6th ed., 2001). WD, MD, PD, and muc, well-, moderately-, poorly-differentiated, and mucinous; MMR: Mismatch repair.

Table 3 Differential gene expression associated with molecular changes and clinicopathological features¹

Parameters	Symbol	Name	Log2 fold changes	Unadjusted P
APC mutations	CDH7	Cadherin 7, type 2	0.419885	0.00033
	DYRK1A	DS tyr-(Y)-phosphorylation regulated kinase 1A	0.326912	0.000343
	SLC19A2	Solute carrier family 19 member 2	-0.48574	0.000427
	PISD	Phosphatidylserine decarboxylase	0.272127	0.000545
	NDUFC1	NADH dehydrogenase 1, subcomplex unknown	0.539581	0.000572
Wnt-activated alterations	PRAF2	PRA1 domain family, member 2	0.620619	0.000205
	FOXF1	Forkhead box F1	-0.93359	0.000524
	CD99L2	CD99 molecule-like 2	0.753489	0.000772
MMR defects	HMGB1	High-mobility group box 1	-0.38141	3.74E-06
	MT1X	Metallothionein 1X	0.965429	0.000252
	MT1A	Metallothionein 1A	1.17894	0.000351
	SUGT1	SGT1, G2 allele of SKP1 (S. cerevisiae)	-0.34799	0.00039
	VTI1B	Vesicle transport with t-SNAREs homolog 1B (yeast)	-0.28513	0.000435
	SST	Somatostatin	1.24407	0.000564
	TDG	Thymine-DNA glycosylase	0.479829	0.000946
RAF-mediated alterations	RAB22A	RAB22A, member RAS oncogene family	-0.36017	0.000289
	PPP1R13L	Protein phosphatase 1, regulatory subunit 13 like	0.823379	0.000614
	CAST	Calpastatin	0.285773	0.000872
Altered p53 expression	HLA-F	Major histocompatibility complex, class I, F	-0.55645	0.000429
	XRCC3	XRCC in Chinese hamster cells 3	-0.26678	0.000588
	CCDC24	Coiled-coil domain containing 24	-0.28995	0.000996
Crossover2	NID2	Nidogen 2 (osteonidogen)	0.938223	0.000214
	EGLN3	egl nine homolog 3 (C. elegans)	0.740933	0.000375
	ITIH1	Inter-alpha (globulin) inhibitor H1	-0.34777	0.0004
	CFH	Complement factor H	-0.33826	0.000542
	ABI3BP	ABI gene family, member 3 binding protein	-0.82558	0.000637
	NIBP	NIK and IKK binding protein	0.649949	0.000688
	SPRR3	Small praline-rich protein 3	0.99738	0.000946
AJCC stage3	PNPT1	Polyribonucleotide nucleotidyltransferase 1	0.716381	4.94E-06
	BAI2	Brain-specific angiogenesis inhibitor 2	0.545369	1.57E-05
	ADCY1	Adenylate cyclase 1 (brain)	-0.43437	1.97E-05
	VEGFC	Vascular endothelial growth factor C	0.329341	9.11E-05
	ATAD3B	ATPase family, AAA domain containing 3B	-0.40978	0.000108
	CAP1	CAP, adenylate cyclase-associated protein 1 (yeast)	-0.66905	0.000405
	RPS6KA6	Ribosomal protein S6 kinase, 90kDa, polypeptide 6	0.301665	0.000586
	FGF5	Fibroblast growth factor 5	0.464162	0.000701
LVN invasion	MMP12	Matrix metallopeptidase 12 (macrophage elastase)	-0.69015	7.76E-05
	RAP1GDS1	RAP1, GTP-GDP dissociation stimulator 1	-0.60949	9.63E-05
	STOML1	Stomatin (EPB72)-like 1	-0.39407	0.000255
	CCL16	Chemokine (C-C motif) ligand 16	0.475838	0.000542
	NOTCH3	Notch homolog 3 (Drosophila)	0.592567	0.000679
	DHPS	Deoxyhypusine synthase	-0.33131	0.000965
Synchronous adenoma	PARP2	Poly (ADP-ribose) polymerase family, member 2	0.573461	6.00E-05
	MRPL21	Mitochondrial ribosomal protein L21	0.243204	0.000149
	MRPL16	Mitochondrial ribosomal protein L16	0.267004	0.000432
	MKKS	McKusick-Kaufman syndrome	0.439584	0.000447
	LHX2	LIM homeobox 2	0.663108	0.000782

¹Differential gene expression in tumor tissues compared to normal epithelia was examined in terms of molecular changes and clinicopathological features, as was considered to be significant when P < 0.001;

²When a tumor carried both APC/Wnt-mediated alterations and MMR defects or RAF-mediated alterations;

³According to the American Joint Committee on Cancer (6th ed., 2001).

Table 4 Class prediction accuracies (%) relative to molecular changes and clinicopathological features

Parameters	Genes1	CCP	DLDA	1-NN	3-NN	NC	SVM	BCCP
Tumor location	620	85	86	92	90	86	94	94
Synchronous adenoma	12	58	60	64	63	57	67	65
Tumor stage	22	62	58	58	60	61	54	60
APC mutations	12	72	72	57	72	67	73	67
LVN invasion	27	70	69	57	60	68	64	68
MMR defects	44	76	77	82	82	76	81	83
p53 alterations	8	65	70	61	73	66	72	79
RAF-mediated alterations	3	36	35	43	51	36	42	69
Wnt-activated alterations	9	54	54	61	61	58	49	54

¹Number of classifier genes. CCP: Compound covariate predictor; DLDA: Diagonal linear discriminant analysis; 1-NN: One nearest-neighbor; 3-NN: Three nearest-neighbor; NC: Nearest centroid; SVM: Support vector machine; BCCP: Bayesian compound covariate predictor; LVN: Lymphovascular or neural.