Proteomics for discovery of candidate colorectal cancer biomarkers

Table 1 Overview of recent proteomic reports focused on the discovery of candidate protein markers for colorectal cancer

Gene	Protein name	Sample	Potential clinical value	Proteomic technique	Validation	Ref.
YWHAZ	14-3-3 protein zeta/delta	Tissue	Tissue biomarker	2-DE, LC-MS/MS	WB	[24,46]
HLA-A1	HLA class I histocompatibility antigen A-1	Membrane fraction of tissue	Tissue biomarker	1-DE, iTRAQ labelling, LC-MS/MS	WB	[105]
ACVR2B	Activin receptor type-2B	Serum	Diagnosis	FP-protein microarray	WB, RP-tissue microarray, ELISA	[78]
PLIN2	Adipophilin	Serum	Diagnosis	Label-free quantitative LC-MS/MS	WB, RP-microarray, IHC	[65]
SPTBN1	Beta-spectrin	Cell lines	Metastasis	1-DE, LC-MS/MS	RNA-Seq	[97]
A1AT	Alpha-1 antitrypsin	Serum, stool	Diagnosis	SELDI-TOF-MS, 1-DE, MudPIT, SRM	-	[69,94]
ORM1	Alpha-1-acid glycoprotein type 1	Serum, stool	Diagnosis	1-DE, MudPIT, SRM	SRM	[77,94]
ORM2	Alpha-1-acid glycoprotein type 2	Serum, stool	Diagnosis	iTRAQ labelling, LC-MS/MS, 1-DE, MudPIT, SRM	WB, ELISA	[73,94]
ENO1	Alpha-enolase	Tissue, validated in serum	Diagnosis	2-DE, 2D-DIGE, LC-MS/MS, MALDI-TOF-MS	WB	[18,19,46]
AFP	Alpha-fetoprotein	Serum	Liver metastasis from CRC	MALDI-TOF-MS, LC-MS/MS	-	[79]
AGT	Angiotensinogen	Serum	Liver metastasis from CRC	MALDI-TOF-MS, LC-MS/MS	-	[79]
ANXA2	Annexin A2	Membrane fractions from colorectal carcinoma	Diagnosis and presumably therapy	2D-DIGE, MALDI-TOF-MS	RP-tissue microarray	[25]
ANXA4	Annexin A4	Membrane fractions from colorectal carcinoma	Diagnosis and presumably therapy	2D-DIGE, MALDI-TOF-MS	RP-tissue microarray	[25,80]
APOA1	Apolipoprotein A1	Serum	Diagnosis	2-DE, 2D-DIGE, MALDI-TOF-MS, LC-MS/MS	WB, RP-protein microarray, RP-tissue microarray	[40,70,80]
CTNNB1	Beta-catenin	Cell lines	Metastasis	1-DE, iTRAQ labelling, LC-MALDI-TOF-MS, LC-MS/MS	WB, RP-tissue microarray, flow cytometry, confocal microscopy	[98,107]
CACYBP	Calcyclin binding protein	Cell lines	Metastasis	iTRAQ labelling, LC-MALDI-TOF-MS	WB	[63,98]
CDH17	Cadherin 17	Membrane fractions from cell lines, exosomes, stool	Metastasis	1-DE, LC-MS/MS	WB, RP-tissue microarray, flow cytometry, confocal microscopy	[91,107,109]
CEACAM5	Carcinoembryonic antigen	Cell lines, membrane fraction from tissue, exosomes, stool	Prognosis	Protein microarray, iTRAQ labelling, 1-DE, LC-MS/MS	WB, RP-tissue microarray, flow cytometry, confocal microscopy, RNA-Seq	[38,91,97,105,107,109]
CAMP	Cathelicidin antimicrobial peptide	Tissue from animal model	Candidate tissue biomarker	2-DE, MudPIT, LC-MS/MS	-	[112]
CTSB	Cathepsin B	Animal model	Candidate diagnosis biomarker	MudPIT, LC-MS/MS	WB, Ab microarray, IHC	[111]
CTSD	Cathepsin D	Tissue, animal model	Candidate diagnosis biomarker	2D-DIGE, MudPIT, LC-MS/MS	WB, Ab microarray, IHC	[80,111]
CDC2	Cell division control protein 2 homolog	Cell lines	Candidate tissue biomarker	2-DE, MALDI-TOF-MS	WB	[95]
CLDN3	Claudin-3	Membrane fraction from tissue, exosomes	Tissue biomarker	1-DE, iTRAQ labelling, LC-MS/MS	WB	[105,108]
PTPRC	Cluster of differentiation 45	Tumor tissue	Diagnosis	Protein microarray	-	[38]
TFRC	Cluster of differentiation 71	Tumor tissue	Diagnosis	Protein microarray	-	[38]
CLU	Clusterin	Serum, animal model	Diagnosis	2-DE, MALDI-TOF-MS, MudPIT, LC-MS/MS	WB, antibody microarray, IHC	[23,70,111]
F5	Coagulation factor V	Animal model	Candidate serum biomarker	Metabolic labelling, LC-MALDI-TOF-MS, SRM, LC-MS-MS	-	[113]
COL6A1	Collagen, type VI α-1 chain	Tissue	Prognosis	LC-MS/MS	WB, IHC	[64]
DPYSL2	Collapsin response mediator protein-2	Secretome from cell lines, validated in serum	Diagnosis	1-DE, MALDI-TOF-MS	WB, IHC, ELISA	[101]
C3	Complement C3	Serum, stool	Diagnosis	SELDI-TOF-MS, 1-DE, MudPIT, SRM, LC-MS/MS	SRM	[69,74,77,94]
C4A	Complement C4-A	Serum	Liver metastasis from CRC	MALDI-TOF MS, LC-MS/MS	-	[79]
C9	Complement C9	Serum	Diagnosis early stage	LC-MS/MS, SRM	RP-protein microarray, SRM	[40,77]
PPIA	Cyclophilin A	Tissue	Tissue biomarker	2-DE, SELDI-TOF-MS	IHC	[58]
CAI	Cytoplasmic carbonic anhydrase I	Tissue	Tissue biomarker	2D-DIGE, MALDI-TOF-MS	WB, IHC	[27,33,84,86]
CAII	Cytoplasmic carbonic anhydrase II	Tissue	Tissue biomarker	2D-DIGE, MALDI-TOF-MS	WB, IHC	[33]
DEFA1	Defensin-1	Tissue, serum, stool	Diagnosis	SELDI-TOF-MS, MALDI-TOF-MS	-	[68,91]
DEFA2	Defensin-2	Tissue, serum	Diagnosis	SELDI-TOF-MS, MALDI-TOF-MS	-	[68]
DEFA3	Defensin-3	Tissue, serum, stool	Diagnosis	SELDI-TOF-MS, MALDI-TOF-MS	-	[68,91]
DES	Desmin	Tissue, validated in serum	Diagnosis and prognosis	2-DE, MALDI-TOF-MS	WB, IHC	[20]
MAPRE1	The adenomatous polyposis coli-binding protein	Tissue	Prognosis	2D-DIGE	IHC	[32]
CDH1	E-cadherin	Secretome from cell lines , serum	Diagnosis	2D-DIGE, MALDI-TOF-MS, LC-MS/MS	WB	[102,103]
EFEMP2	EGF-containing fibulin-like extracellular matrix protein 2	Secretome of cultured fresh normal and CRC tissues	Diagnosis	1-DE, LC-MS/MS	WB, IHC	[13]
EFNB2	Ephrin-B2	Exosomes	Metastasis	1-DE, LC-MS/MS	-	[108,110]
EGFR	Epidermal growth factor receptor	Cell lines, exosomes	Candidate diagnosis biomarker	1-DE, LC-MS/MS	WB, RP-tissue microarray, flow cytometry, confocal microscopy, RNA-Seq	[97,107,109]
EPCAM	Epithelial cell surface adhesion molecule	Exosomes	Candidate diagnosis biomarker	LC-MS/MS	-	[109]
GSPT2	Eukaryotic peptide chain release factor GTP-binding subunit	Serum	Liver metastasis from CRC	MALDI-TOF-MS, LC-MS/MS	-	[79]
XPO4	Exportin	Cell lines	Tissue biomarker	1-DE, LC-MS/MS	RNA-Seq	[97]
EZR	Ezrin	Cell lines	Tissue biomarker	1-DE, LC-MS/MS	RNA-Seq	[97]
FABP1	Fatty acid-binding protein 1	Tissue	Prognosis	2D-DIGE, ICAT, LC-MS/MS	WB, IHC	[62]
FGFR4	Fibroblast growth factor receptor 4	Serum	Diagnosis	FP-protein microarray	-	[78]
FGA	Fibrinogen alpha	Serum, stool	Liver metastasis from CRC, diagnosis	MALDI-TOF MS, LC-MS/MS, 1-DE, MudPIT, SRM	-	[79,94]
BLVRB	Flavin reductase	Tissue	Tissue biomarker	2-DE, SELDI-TOF-MS	IHC	[58]
LGALS3	Galectin 3	Cell lines	Tissue biomarker	2-DE, MALDI-TOF-MS	WB	[95]
LGALS4	Galectin 4	Exosomes	Tissue biomarker	1-DE, LC-MS/MS	-	[108]
GSN	Gelsolin	Tissue, serum	Diagnosis	2D-DIGE, MALDI-TOF-MS, SRM, LC-MS/MS	WB, IHC	[19,77]
GSTA1	Glutathione S-transferase alpha-1	Cell lines	Tissue biomarker	2-DE, MALDI-TOF-MS, LC-MS/MS	WB	[95,96]
GPA33	Glycoprotein A33	Exosomes	Candidate diagnosis biomarker	Immunoaffinity capture microbeads and LC-MS/MS	-	[109]
GDF15	Growth/differentiation factor 15	Secretome from cell lines, validated in serum	Metastasis	LC-MS/MS	WB, ELISA	[71]
HBG	Haemoglobin	Stool	Diagnosis	1-DE, MudPIT, SRM	Immunoassay	[93,94]
HSPA9	Heat shock 70 kDa protein 9 (mortalin)	Cell lines	Tissue biomarker	1-DE, LC-MS/MS	RNA-Seq	[97]
HSPB1	Heat shock protein 27	Tissue, validated in serum	Diagnosis	2-DE, LC-MS/MS	-	[18]
HSPD1	Heat shock protein 60	Serum	Diagnosis of late stage CRC, prognosis?	2D-DIGE, MALDI-TOF-MS	WB, ELISA, Tissue microarray	[72]
HNRNPH2	Heterogeneous nuclear ribonucleoprotein H2	Nuclear fraction from tissue	Tissue biomarker	1-DE, MALDI-TOF-MS, LC-MS/MS	-	[104]
HNRNPA1	Heterogeneous nuclear ribonucleoprotein A1	Tissue, validated in serum	Diagnosis and prognosis	2-DE , MALDI-TOF-MS, SELDI-TOF-MS	IHC	[58,87]
HNRNPH3	Heterogeneous nuclear ribonucleoprotein H3	Cell lines	Tissue biomarker	2-DE, MALDI-TOF-MS	WB	[95]
HABP2	Hyaluronan-binding protein 2	Serum	Diagnosis	SRM, LC-MS/MS	-	[77]
ITLN1	Intelectin-1	Tissue	Prognosis	2D-DIGE, ICAT, LC-MS/MS	WB, IHC	[62]
ITIH3	Inter-alpha-trypsin inhibitor heavy chain 3	Serum from animal model	Serum biomarker	Metabolic labelling, LC-MALDI-TOF-MS, SRM, LC-MS-MS	-	[113]
IL8	Interleukin 8	Animal model	Candidate tissue biomarker	2-DE, MudPIT, LC-MS/MS	-	[112]
JAG1	Jagged 1 protein	Exosomes	Metastasis	1-DE, LC-MS/MS	-	[110]
JUP	Junction plakoglobin	Membrane fraction from cell lines, tissue	Diagnosis, prognosis and metastasis	1-DE, LC-MS/MS	WB, RP-tissue microarray, flow cytometry, confocal microscopy	[64,107]
KRT5	Keratin 5	Tissue, cell lines	Prognosis	LC-MS/MS, 2-DE, iTRAQ labelling, LC-MALDI-TOF-MS	WB, IHC	[64,98]
KNG1	Kininogen-1	Serum, tissue	Diagnosis	MB-WCX, MALDI-TOF-MS	ELISA, IHC	[76]
MIF	Macrophage migration inhibitory factor	Tissue, validated in serum	Diagnosis	2-DE, LC-MS/MS	-	[18]
MGAM	Maltase-glucoamylase	Serum from animal model	Candidate serum biomarker	Metabolic labelling, LC-MALDI-TOF-MS, SRM, LC-MS-MS	-	[113]
MAPKAPK3	MAP kinase-activated protein kinase 3	Serum	Diagnosis	FP-protein microarray	WB, RP-tissue microarray, ELISA	[78]
MET	Met-proto-oncogen	Cell lines, exosomes	Metastasis	1-DE, LC-MS/MS	RNA-Seq	[97,110]
PRTN3	Myeloblastin	Stool	Diagnosis	1-DE, MudPIT, SRM	Immunoassay	[94]
MNDA	Myeloid cell nuclear differentiation antigen	Nuclear fraction from tissue	Tissue biomarker	na1-DE, MALDI-TOF-MS, LC-MS/MS	-	[104]
MYH10	Myosin 10	Cell lines	Candidate tissue biomarker	iTRAQ labelling, LC-MALDI-TOF-MS	WB	[98]
MARCKS	Myristoylated alanine-rich C-kinase substrate	Cell lines	Candidate tissue biomarker	iTRAQ labelling, LC-MALDI-TOF-MS	WB	[98]
NCAM1	Neural cell adhesion molecule 1	Cell lines	Candidate tissue biomarker	iTRAQ labelling, LC-MALDI-TOF-MS	WB	[98]
NNMT	Nicotinamide N-methyltransferase	Tissue, validated in serum	Diagnosis	2-DE, MALDI-TOF-MS	WB, ELISA	[46]
NUP62	Nuclear pore complex 62	Nuclear fraction from tissue	Tissue biomarker	1-DE, MALDI-TOF-MS, LC-MS/MS	-	[104]
NUP88	Nuclear pore complex 88	Nuclear fraction from tissue	Tissue biomarker	1-DE, MALDI-TOF-MS, LC-MS/MS	-	[104]
NPM1	Nucleophosmin	Cell lines	Candidate tissue biomarker	1-DE, LC-MS/MS	-	[97]
NME1	Nucleoside diphosphate kinase A	Tissue, cell lines, serum	Diagnosis	2-DE, 2D-DIGE, RP-tissue microarray, MALDI-TOF-MS, LC-MS/MS	WB, IHC	[4,19,20,24,39,46,84]
NME2	Nucleoside diphosphate kinase B	Tissue	Tissue biomarker	2-DE, SELDI-TOF-MS	IHC	[58]
OLFM4	Olfactomedin-4	Secreted proteins from tissue	Tissue biomarker	OFFGEL, iTRAQ labelling, MALDI-TOF-MS	IHC	[88]
PARK7	Parkinson protein 7	Tissue, animal model	Tissue biomarker	2-DE, LC-MS/MS	WB, IHC	[24,111]
PRDX2	Peroxiredoxins 2	Cell lines	Candidate tissue biomarker	2D-DIGE, MALDI-TOF-MS, LC-MS/MS	WB	[102]
PRDX6	Peroxiredoxins 6	Cell lines	Candidate tissue biomarker	2D-DIGE, MALDI-TOF-MS, LC-MS/MS	WB	[102]
PGK1	Phosphoglycerate kinase I	Cell lines	Candidate tissue biomarker	2-DE, MALDI-TOF-MS	WB	[95]
ADCYAP1	Pituitary adenylate cyclase-activating polypeptide	Tissue	Tissue biomarker	2-DE, SELDI-TOF-MS	IHC	[58]
PCNA	Proliferating cell nuclear antigen	Cell lines	Candidate tissue biomarker	2-DE, MALDI-TOF-MS	WB	[95]
PSME3	Proteasome activator complex subunit 3	Tissue, validated in serum	Diagnosis and prognosis	2-DE, MALDI-TOF-MS	IHC	[46,47]
RBBP4	Retinoblastoma binding protein 4	Cell line, tissue	Candidate tissue biomarker	2-DE, LC-MS/MS	WB	[24]
ARHGDI	Rho GDP-dissociation inhibitor	Tissue, cell lines	Metastasis	2-DE, MALDI-TOF-MS		[21]
S100A11	S100-A11 calcium binding protein	Tissue	Tissue biomarker	2-DE, SELDI-TOF-MS	IHC, protein microarray	[58,59]
S100A12	S100-A12 calcium binding protein	Tissue, stool, validated in serum	Diagnosis	2-DE, MALDI-TOF-MS, LC-MS/MS	Immunoassay	[48,93]
S100A6	S100-A6 calcium binding protein	Membrane fraction from tissue	Tissue biomarker	1-DE, 2-DE, MALDI-TOF-MS, LC-MS/MS	-	[81,110]
S100A8	S100-A8 calcium binding protein	Tissue, cell lines, exosomes, validated in serum, stool	Diagnosis	1-DE, 2D-DIGE, MALDI-TOF-MS, LC-MS/MS	WB, IHC	[19,84,91,110]
S100A9	S100-A9 calcium binding protein	Tissue, cell lines, exosomes, animal model, validated in serum, stool	Diagnosis	1-DE, 2D-DIGE, MALDI-TOF-MS, LC-MS/MS	WB, IHC	[19,84,85,91,110]
SELENBP1	Selenium binding protein 1	Tissue, cell lines, serum	Prognosis	2D-DIGE, MALDI-TOF/TOF, and MALDI-TOF-MS	WB	[19,84,86]
PIM1	Serine/threonine-protein kinase Pim-1	Serum	Diagnosis	FP-protein microarray	WB, RP-tissue microarray, ELISA	[78]
SAA2	Serum amyloid A-2 protein	Serum	Diagnosis	1-DE, MudPIT, LC-MS/MS	SRM	[77]
TAGLN	Smooth muscle protein 22-alpha	Tissue	Tissue biomarker	2-DE, SELDI-TOF-MS	IHC	[58]
SPTAN1	Spectrin	Cell lines	Candidate tissue biomarker	1-DE, LC-MS/MS	RNA-seq	[97]
SRC	Proto-oncogene tyrosine-protein kinase Src	Serum, exosomes	Diagnosis, metastasis	FP-protein microarray, 1-DE, LC-MS/MS	WB, RP-tissue microarray, ELISA	[78,110]
STMN1	Stathmin	Cell lines	Metastasis	iTRAQ, LC-MALDI-TOF-MS	WB	[98]
STOML2	Stomatin-like protein 2	Tissue, serum	Diagnosis and prognosis	LC-MS/MS	ELISA	[106]
TNC	Tenascin C	Exosomes	Metastasis	1-DE, LC-MS/MS	-	[110]
TRIP	Thryroid receptor interactor	Serum	Diagnosis	2D-DIGE, MALDI-TOF MS	-	[30]
TIMP1	TIMP metallopeptidase inhibitor 1	Serum	Diagnosis	Lectin Fractionation, MALDI-MS-MS	SRM	[75]
TLRs	Toll-like receptors	Animal model	Candidate tissue biomarker	2-DE, MudPIT, LC-MS/MS	-	[112]
TNIK	TRAF2 and NCK-interacting protein kinase	Exosomes	Metastasis	1-DE, LC-MS/MS	-	[110]
TALDO1	Transaldolase 1	Serum	Diagnosis	2D-DIGE, MALDI-TOF MS	-	[30]
TFRC	Transferrin	Serum, stool	Diagnosis	SELDI-TOF-MS, 1-DE, MudPIT, SRM	-	[69,94]
TGFBI	Transforming growth factor β-induced protein ig-h3	Cell lines	Candidate serum biomarker	2-DE, 2D-DIGE, MALDI-TOF-MS	-	[35,46]
TAGLN	Transgelin	Tissue	Prognosis	2D-DIGE, ICAT, LC-MS/MS	WB, IHC	[62]
TPT1	Translationally controlled tumour protein	Secretome from cell lines, tissue	Candidate serum biomarker	2D-DIGE, MALDI-TOF-MS	-	[35,84]
TTR	Transthyretin	Serum	Metastasis	2-DE, MALDI-TOF MS	ELISA	[11]
TFF3	Trefoil factor 3	Secretome from cell lines, tissue, validated in serum	Metastasis	LC-MS/MS	WB, ELISA	[71]
TREM1	Triggering receptor expressed on myeloid cells 1	Animal model	Candidate tissue biomarker	2-DE, MudPIT, LC-MS/MS	-	[112]
TPM2	Tropomyosin 2 (beta chain)	Tissue	Prognosis	2D-DIGE, ICAT, LC-MS/MS	WB, IHC	[62]
TUBB	Tubulin beta chain	Tissue, cell lines	Diagnosis and prognosis	2DE, iTRAQ labelling, LC-MALDI-TOF-MS, LC-MS/MS,	WB, IHC	[64,98]
PKM	Pyruvate kinase type M2	Tissue, stool	Diagnosis	2D-DIGE, MALDI-TOF-MS	-	[19,92]
VCP	Valosin-containing protein	Tissue	Prognosis	2D-DIGE, ICAT, LC-MS/MS	WB, IHC	[62]
VIL1	Villin 1	Tissue, cell lines	Metastasis	iTRAQ labelling, 2-DE, 2D-DIGE, LC-MALDI-TOF-MS, MALDI-TOF-MS	WB	[19,95,98]
VDAC1	Voltage-dependent anion-selective channel protein 1	Membrane fraction from colorectal carcinoma	Diagnosis and presumably therapy	2D-DIGE, MALDI-TOF MS	RP-tissue microarray	[25]

CRC: Colorectal cancer; 2-DE: Two-dimensional electrophoresis; LC: Liquid chromatography; MS: Mass spectrometry; SELDI-TOF-MS: Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry; MudPIT: Multidimensional protein identification technology; SRM: Selected reaction monitoring; ELISA: Enzyme-linked immunosorbent assay; IHC: Immunohistochemistry.