Current application of proteomics in biomarker discovery for inflammatory bowel disease

Table 1 Current biomarkers and their utility in inflammatory bowel disease management[12]

Application	Biomarker	Utility
Diagnosis of IBD	Fecal calprotectin[69]	Sensitivity: 89%-98%, specificity: 81%-91%
	Fecal lactoferrin[70]	Sensitivity: 80%, specificity: 82%
	Fecal 100A12[71] (differentiating from IBS)	Sensitivity: 86%, specificity: 96%
	CRP[72-74]	Sensitivity: Approximately equal 100% in CD, approximately equal 50% in UC poor specificity
Distinguishing UC and CD	ASCA[75]	Sensitivity: 40%-50%, specificity: > 90% in CD
	pANCA[75]	Sensitivity: 57%, specificity: 92%
	Escherichia coli antibodies (Anti-OmpC, Anti-I2, Anti-CBir1)[76]	Sensitivity: 18%-55%, specificity: 76%-93%[76]
Marker of disease activity	Fecal lactoferrin[77,78]	Sensitivity: 66%-80%
		Specificity: 60%-100%
	Fecal calprotectin[77,78]	Sensitivity: 70%-100%
		Specificity: 44%-100%
	CRP[78]	Sensitivity: 48%
		Specificity: 91%
Assessing mucosal healing	Fecal calprotectin	Several studies demonstrate significant reduction in biomarker in the presence of mucosal healing with treatment
Predicting disease course	Fecal lactoferrin[77]	May be associated with complications including; structuring or fistulising disease, and small bowel disease pANCA may predict aggressive UC and pouchitis following surgery[79]
	ASCA
	pANCA Anti-I2, Anti-OmpC[12]
Predicting Relapse within 12 mo	Fecal calprotectin[80,81]	Sensitivity: 69%-90%
		Specificity: 69%-82%
		Positive predictive value: 81%/87% (UC/CD)
		Negative predictive value: 90%/43% (UC/CD)
	Fecal lactoferrin[81]	Sensitivity: 62%
		Specificity: 65%
Predicting therapeutic response	pANCA[82]	Conflicting reports, possible lower response rate to infliximab in patients with a positive serology
	Anti-I2[83]	94% responded to fecal diversion

CD: Crohn’s disease; UC: Ulcerative colitis; IBD: Inflammatory bowel disease; ASCA: Anti-Saccharomyces cerevisiae; pANCA: Perinuclear antineutrophil cytoplasmic antibodies; CRP: C-Reactive protein; PF4: Platelet factor 4.

Table 2 Proteomic studies for discovering diagnostic inflammatory bowel disease biomarkers

Ref.	Bio-sample	Sample size	Proteomic technique	Results
Meuwis et al[22]	Serum	CD: 30	SELDI-TOF	4 candidate proteins selected for high diagnostic value; PF4, MRP8, FIBA, Hpα 2. PF4 and Hpα 2 were also confirmed and correlated using ELISA and immunoblotting
		UC: 30
		Inflammatory control: 30
		Healthy controls: 30
Kanmura et al[23]	Blood	CD: 22	SELDI-TOF	Plasma concentrations of HNP1, 2 and 3 were significantly higher in active UC compared to inactive UC, CD and control patients
		UC: 48
		Colorectal Cancer: 5
		Infectious colitis: 6
		Healthy controls: 13
Hatsugai et al[24]	Blood	CD: 13	2-DE	Multivariate analysis of peripheral blood mononuclear cells protein profile 58 protein) allowed for accurate discrimination between UC and CD
		UC: 17	MALDI-TOF
		Healthy controls: 17
Nanni et al[25]	Blood	Healthy controls: 48	Liquid chromatography quadrupole-TOF	Exopeptidase activity may distinguish CD from UC. Label free method developed could accurately distinguish synthetic spiked samples of serum
		CD: 15	SELDI-TOF
Sumramanian et al[26]	Serum	CD: 48		Protein signature of 12 mass: Charge peaks could classify CD with approximately equal 95% sensitivity/specificity
		UC: 62		4 proteins identified as clinically useful
Nanni et al[27]	Serum	Healthy controls: 48	Solid-phase extraction MALDI-TOF	20 protein signals could be used to accurately classify IBD patients
		CD: 15
		UC: 26
Vaiopoulou et al[28]	Serum	CD: 24 (12 adults, 12 children)	2-DE	Clusterin was found to be overexpressed in adult CD. Ceruloplasmin and apolipoprotein B-100 was over-expressed in children
			MALDI-TOF
Han et al[34]	Intestinal biopsy	CD: 3	Liquid chromatography quadrupole-TOF	Increased in UC: TTBK2, SYNE2, SUCLG2, POSTN
		UC: 4		Up-regulated in CD: ANXA2, EPX, LAP3, RDX
		Inflammatory polyps: 2		Up-regulated in IBD: S100A8, MPO, DEFA1B
				Up-regulated in CD (P < 0.05 AND > 2x increase): PRG2, LCP1, PSME1
		Normal colon: 3
M’koma et al[35]	Colon samples	CD: 27	Histology directed MALDI-TOF	5 m:z peaks were identified and cross-validated for the differentiation of UC and CD
		UC: 24
Seeley et al[36]	Colon samples	CD: 26	Histology directed MALDI-TOF	Using a support vector machine and 25 m:z peaks, UC and CD cases were predicted in 93.3% and 60.4% respectively. A lower spectral accuracy cut-off increased sensitivity
		UC: 36
Wasinger et al[39]	Serum	UC: 27	MRM	SPP24 differentiated IBD patients from healthy controls
		CD: 56		α-1-microglobulin distinguished patients with UC in remission from healthy controls
		Controls: 14
		RA controls: 12

CD: Crohn’s disease; UC: Ulcerative colitis; IBD: Inflammatory bowel disease; MRM: Multiple reaction monitoring; PF4: Platelet factor 4; MRP8: Myeloid related protein 8; FIBA: Fibrinopeptide A; Hpα2: Haptoglobin α2.

Table 3 Proteomic studies for discovering inflammatory bowel disease management biomarkers

Ref.	Bio-sample	Sample size	Proteomic technique	Results
Disease activity biomarkers
Han et al[34]	Intestinal tissue	CD: 3	LC-QTOF	16 proteins distinguishing active/inactive CD
		UC: 4		4 proteins distinguishing active/inactive UC
		Inflammatory Polyps: 2
		Normal colon: 3
Wasinger et al[39]	Serum	UC: 27	MRM	SPP24 was able to differentiate active and quiescent disease in both UC and CD
		CD: 56
		Controls: 14
		RA controls: 12
Prognostic biomarkers
May et al[57]	Intestinal epithelial cells	Non-dysplastic tissue from non-progressors: 5	High-performance liquid chromatography quadrupole -TOF	155 candidate proteins were expressed differentially by > 2x between dysplastic/cancerous and non-dysplastic UC tissue. They were identified as mitochondrial, cytoskeletal, apoptotic and RAS superfamily proteins
		Non-dysplastic tissue from progressors: 5
		Highly dysplastic tissue from UC progressors: 5
Response to therapy biomarkers
Meuwis et al[37]	Serum	Infliximab responders: 40	SELDI-TOF	3 proteins (PF4, sCD40L and IL-6) were identified infliximab non-responders, although PF4 and sCD40L could not be confirmed or correlated with ELISA
		Infliximab non-responders: 40
Kanmura et al[23]	Blood samples	CD: 22	SELDI-TOF	Plasma concentration of HNP1, 2 and 3 decreased following successful corticosteroid therapy compared to non-responders
		UC: 48
		Colorectal cancer: 5
		Infectious colitis: 6
		Healthy controls: 13
Gazouli et al[38]	Serum	Infliximab responders: 6	2-DE, MALDI-TOF	7 proteins were increased in CD patients who did not achieve remission on infliximab. 4 were increased in patients who achieved remission. 3 proteins were lower in remission patients
		Infliximab non-responders: 6
		Infliximab partial responders: 6

CD: Crohn’s disease; UC: Ulcerative colitis; IBD: Inflammatory bowel disease; MRM: Multiple reaction monitoring.