Proteome profiling of spinal cord and dorsal root ganglia in rats with trinitrobenzene sulfonic acid-induced colitis

Table 1 Significantly regulated proteins after trinitrobenzene sulfonic acid-induced colitis in dorsal root ganglia

Function	Cell component	Protein name	Abbreviation	AccessionNo.	TheoreticalPI/Mr (kDa)	SequenceCoverage (%)	MASSOT score	Change(TNBS)
Proteins involved in inflammatory/immune response
Autoantigen in many autoimmune diseases	Cytoplasm, nucleus spliceosome	Isoform B0a of heterogeneous nuclear ribonucleoproteins A2/B1	Hnrnpa2b1	IPI00923129	8.74/32 572	16	220	↑
Hemopexin	Secreted	Hemopexin	Hpx	IPI00195516	7.58/52 060	22	597	↑
1. Accelerate the folding of protein 2. Immunosuppression	Cytosol, nucleus	Peptidyl-prolyl cis-trans isomerase A	Ppia	IPI00387771	8.34/18 091	32	363	↓
Proteins involved in cell signaling
Growth protein	Membrane	Adenylyl cyclase-associated protein 1	Cap1	IPI00555187	7.16/51 899	5	145	↑
Cytoplasmic tetramerisation domain of voltage-gated K+ channel		Similar to potassium channel tetramerisation domain containing protein 12	Kctd12	IPI00359734	8.95/47 077	16	192	↑
1. Ion channel 2. Mitochondrial apoptosis	Mitochondrial outer membrane	Voltage-dependent anion-selective channel protein 2	Vdac2	IPI00198327	7.44/32 353	9	76	↓
Proteins involved in redox regulation
Cell redox homeostasis	Mitochondria	Dihydrolipoyl dehydrogenase, mitochondrial	Dld	IPI00365545	7.96/54 574	5	141	↑
Antioxidant	Mitochondria	Superoxide dismutase [Mn], mitochondrial	Sod2	IPI00211593	8.96/24 887	22	130	↓
Xenobiotic metabolism and cellular defense	Nucleus	Glutathione S-transferase P	Gstp1	IPI00231229	6.89/23 652	12	255	↓
Eliminating peroxides	Mitochondria, cytosol	Peroxiredoxin-1	Prdx1	IPI00211779	8.27/22 323	9	108	↓
Proteins involved in chaperone function
Chaperonins/heat shock proteins	Mitochondria	Heat shock cognate 71 kDa protein	Hspa8	IPI00208205	5.37/71 055	18	304	↓
Chaperonins/heat shock proteins	Nucleus, cytoplasm	Stress-induced-phosphoprotein 1	Stip1	IPI00213013	6.40/63 158	9	156	↑
Proteins involved in cellular structure
Component of the nuclear lamina	Insoluble fraction, lamin filament, nuclear matrix	Lamin C2	Lmna	IPI00188879	6.22/52 661	16	136	↑
Proteins involved in cellular metabolism
Oxidoreductase in valine and pyrimidine catabolic pathways	Mitochondria	Methylmalonate-semialdehyde dehydrogenase [acylating],mitochondrial	Aldh6a1	IPI00205018	8.44/58 396	4	68	↓
Glycolytic enzyme	Mitochondria	Fructose-bisphosphate aldolase A	Aldoc	IPI00231734	8.31/39 783	11	148	↓
Glycolytic enzyme	Axon, mitochondria	Aldoc 17 kDa protein	Aldoc	IPI00561972	6.84/16 666	14	88	↓
Glycolytic enzyme	Mitochondria	Dihydrolipoyllysine-residueacetyltransferase component of pyruvate dehydrogenase complex	Dlat	IPI00231714	8.76/67 637	7	79	↑
Glycolytic enzyme	Cytoplasm	Phosphoglycerate kinase 1	Pgk1	IPI00231426	8.02/44 909	16	184	↓
Glycolytic enzyme		Similar to pyruvate kinase 3		IPI00561880	7.15/58 264	17	231	↓
Glycolytic enzyme	Nucleus cytoplasm	Isoform M1 of pyruvate kinase isozymes M1/M2	Pkm2	IPI00231929	6.63/58 452	22	491	↑
1. Glycolytic enzyme 2. Transcription activation 3. Initiation of apoptosis	Cytoplasm	Similar to glyceraldehyde-3-phosphate dehydrogenase	RGD1565368	IPI00554039	8.44/36 045	14	347	↑
ATP energy transduction	Cytoplasm	Creatine kinase M-type	Ckm	IPI00211053	6.58/43 246	19	361	↑
ATP transducing	Mitochondria	Creatine kinase, mitochondrial 1, ubiquitous	Ckmt1	IPI00555166	8.58/47 331	21	231	↓
TCA cycle	Mitochondria	Isoform mitochondrial of fumarate hydratase, mitochondrial	Fh1	IPI00231611	9.06/54 714	5	115	↓
1. TCA cycle 2. Gluconeogenesis 3. Antioxidant	Mitochondria	Malate dehydrogenase, mitochondrial	Mdh2	IPI00197696	8.93/36 117	11	90	↓
Extrahepatic ketone body catabolism	Mitochondria	3-ketoacid-coenzyme A transferase 1, mitochondrial	Oxct1 Succinyl-CoA	IPI00766788	8.7/56 624	6	116	↑

↑: Elevated protein expression in TNBS group compared with saline group; ↓: Decreased protein expression in TNBS group in comparison with saline group. DRG: Dorsal root ganglia; TNBS: Trinitrobenzene sulfonic acid; Hnrnpa2b1: Heterogeneous nuclear ribonucleoproteins A2/B1; Cap1: Cyclase-associated protein 1; Kctd12: Potassium channel tetramerisation domain containing protein 12; Vdac2: Voltage-dependent anion-selective channel protein 2; Dld: Dihydrolipoyl dehydrogenase; Sod2: Superoxide dismutase; Gstp1: Glutathione S-transferase P; Prdx1: Peroxiredoxin-1; Stip1: Stress-induced phosphoprotein 1; Lmna: Lamin C2; Ckm: Creatine kinase M-type; Ckmt1: Creatine kinase, mitochondrial 1, ubiquitous; Fh1: Fumarate hydratase; Mdh2: Malate dehydrogenase; Oxct1 Succinyl-CoA: 3-ketoacid-coenzyme A transferase 1.

Table 2 Proteins significantly regulated after trinitrobenzene sulfonic acid-induced colitis in spinal cord

Function	Cell component	Protein name	Abbreviation	AccessionNo.	TheoreticalPI/Mr (kDa)	Sequencecoverage(%)	MASSOTscore	Change(TNBS)
Proteins involved in inflammatory/immune response
1. Fatty acid catabolic process 2. Play a role in eicosanoid synthesis and inflammation	Cytoplasm	Isoform 1 of cytosolic acyl coenzyme A thioester hydrolase	Acot7	IPI00213571	7.16/37 936	14	167	↓
1. Glycolytic enzyme 2. Autoantigen	Cell membrane, cytoplasm	α-enolase	Eno1	IPI00464815	6.16/47 440	13	183	↓
Immunity	Cytoplasm, nucleus	Proteasome subunit α type-1	Psma1	IPI00191748	6.15/29 784	17	193	↓
Proteins involved in cell signaling
1. Growth protein 2. Modulate calcium influx 3. Regulate the release of ICGRP	Cytoplasm	Dihydropyrimidinase-related protein 2	Dpysl2	IPI00870112	5.95/62 638	16	270	↑
Calcium ion signaling	Cytoplasm, cytoskeleton	Troponin C-like protein		gi223036	4.12/16 696	10	91	↓
1. Cell division 2. Apoptosis 3. Regulate insulin sensitivity	Melanosome, cytoplasm	14-3-3 protein epsilon	Ywhae	IPI00325135	4.63/29 326	15	165	↑
Proteins involved in sulfate transport
Transferase detoxification	Mitochondrial matrix	Thiosulfate sulfurtransferase	Tst	IPI00366293	7.71/33 614	25	333	↓
Proteins involved in redox regulation
Xenobiotic metabolism and cellular defense	Nucleus	Glutathione S-transferase P	Gstp1	IPI00231229	6.89/23 652	20	263	↓
Proteins involved in chaperone function
Assist protein folding	Cytoplasm	T-complex protein 1 subunit γ	Cct3	IPI00372388	6.23/61 179	8	122	↑
Chaperonins/heat shock proteins	Mitochondria	Heat shock cognate 71 kDa protein	Hspa8	IPI00208205	5.37/71 055	11	172	↑
Chaperonins/heat shock proteins	Cytoplasm, nucleus	Stress-induced-phosphoprotein 1	Stip1	IPI00213013	6.4/63 158	7	143	↑
Proteins involved in cellular metabolism
Glycolytic enzyme	Axon, mitochondria	Fructose-bisphosphate aldolase C	Aldoc	IPI00231736	6.67/39 658	10	189	↓
Glycolytic enzyme	Cytoplasm	Similar to phosphoglycerate kinase 1	RGD1560402	IPI00372910	6.15/43 604	10	151	↑
1. Glycolytic enzyme 2. Transcription activation 3. Initiation of apoptosis	Cytoplasm	Similar to glyceraldehyde-3-phosphate dehydrogenase	RGD1565368	IPI00554039	8.44/36 045	18	454	↑
ATP transducing	Mitochondria	Creatine kinase, mitochondrial 1, ubiquitous	Ckmt1	IPI00555166	8.58/47 331	12	155	↑
1. Electron transport in respiratory chain 2. Oxidoreductase	Mitochondria	NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial	Ndufv2	IPI00367152	6.23/27 703	24	253	↑
Electron transport in respiratory chain	Membrane, mitochondria	NADH dehydrogenase (ubiquinone) 1 β subcomplex, 10	Ndufb10	IPI00202238	7.57/21 131	32	306	↓
1. Electron transport in respiratory chain 2. Mitochondrial dysfunction	Mitochondrial	Cytochrome b-c1 complex subunit 2, mitochondrial	Uqcrc2	IPI00188924	9.16/48 423	8	222	↓
Amino-acid (serine) biosynthesis		Phosphoserine aminotransferase	Psat1	IPI00331919	7.57/40 943	8	97	↓

↑: Elevated protein expression in TNBS group compared with saline group; ↓: Decreased protein expression in TNBS group in comparison with saline group; TNBS: Trinitrobenzene sulfonic acid; NADH: Nicotinamide adenine dinucleotide; Psma1: Proteasome subunit α type-1; Dpysl2: Dihydropyrimidinase-related protein 2; Ywhae: The 14-3-3 protein epsilon; Tst: Thiosulfate sulfurtransferase; Gstp1: Glutathione S-transferase P; Hspa8: Heat shock cognate 71 kDa protein; Stip1: Stress-induced phosphoprotein 1; Aldoc: Aldolase C; Ckmt1: Creatine kinase mitochondrial 1 ubiquitous; Ndufv2: NADH dehydrogenase (ubiquinone) flavoprotein 2; Ndufb10: NADH dehydrogenase (ubiquinone) 1 β subcomplex 10; Uqcrc2: Cytochrome b-c1 complex subunit 2; Psat1: Phosphoserine aminotransferase.

Table 3 Differentially expressed proteins identified in cellular and animal models of inflammatory bowel disease and in clinical samples of inflammatory bowel disease patients

Ref.	Animalmodel	Cell	Patient	Sample	Analytical technique (S)	No. of regulatedproteins	Major findings	Protein name	Change
[68]		Human adenocarcinoma cells Dld-1 exposed to interferon-γ, interleukin-1 and interleukin-6			2D PAGE-MALDI-TOF-MS/MS	5	Protein biosynthesis	Tryptophanyl-tRNA synthetase	Up
							Redox regulation	Indoleamine-2, 3-Dioxygenase	Up
[14]		HT29 Cl.16E cell treated with interferon-γ			1D PAGE-LC ESI/QTOF-MS/MS	7	Structure protein	Histone H2A type-1B	Up
							Metabolic enzymes	Adenosylhomocysteinase	Up
							Redox regulation	Peroxiedonxin-1	Down
			CD patients	Intestinal epithelial cells		14	Structure protein	Histone H1.2, H2A.V, H2B Type 1-C/E/F/G/I, H3 Like, H4	Up
							Chaperone	Heat shock 70 kDa protein 5	Up
							Annexin	Annexin A1	Down
[69]			CD and UC patients	Endoscopic biopsies of colonic mucosa	Multi-epitope-ligand-cartographic immunofluorescence microscopy		Apoptosis	Caspase-3	Down
							Transcription regulation	NF-κ B	Up
[12]			UC patients	Colon biopsies	2D-MALDI-TOF-MS/MS	19	Negative regulation of cell proliferation and DNA replication	Prohibitin (PHB)	Down
							1. TCA Cycle 2. Gluconeogenesis 3. Antioxidant	Mitochondrial malate dehydrogenase (Mdh2)	Down
							Eliminating Peroxides	Thioredoxin peroxidase (Prdx1)	Down
							1. Ion Channel 2. Apoptosis	Voltage-dependent anion-selective channel protein 1 (Vdac1)	Down
							1. Intracellular signal transduction 2. Regulation of transcription, DND-dependent	Nuclear factor of activated T-cells cytoplasmic (NFAT C1)	Up
							Protein folding	Tumor rejection antigen 1 (TRA1)	Up
							Cell adhesion Host-virus interaction	Poliovirus receptor related protein 1 (PVRL1)	Up
[70]			CD and UC patients	Serum	SELDI-TOF-MS	4	Cytokine-mediated signaling	Platelet factor 4	Up
							Chronic inflammation	Myeloid related protein 8	Up
							Fibrin producing and inflammation	FIBA	Up
							Transferase	Haptoglobin alph2	Up
[71]			CD and UC patients	Intestinal epithelial cells	2D PAGE-MALDI-TOF-MS	17	Regulation of GTPase activity	Rho gdp dissociation inhibitor (GDI) α chain	Up
							Differentiation	Nicotinamide phosphor-ribosyltransferase	Up
							Calcium ion binding	Myosin regulatory light chain 2, nonsarcomeric	Up
[72]			CD patients	Serum	RP NANO-LC ESI/Q-TOF MS	8	Immunity	Complement C3	Up
							Blood coagulation	Fibrinogen α chain	Up
							Lipid transport	Apolipoprotein E	Down
[73]			UC patients	Mucosa/ submucosa	2D PAGE- LC-MS/MS	7	Cell adhesion	Protocadherin 17 precursor	Up
							Acute-phase response	α-1-Antitrypsin (precursor)	Up
							Muscle protein	Caldesmon	Up
							Structural molecule activity	Mutant desmin	Up
[74]	DSS treated Balb/C mice			Mucosa	2D-DIGE- MALTI-TOF	5	Isomerase	Protein disulfide isomerase family A, member 3	Down
							Redox regulation	Peroxiredoxin 6 (Prx6)	Down
[13]	TNBS treated SD rats			Lymphocytes	2D-MALDI- TOF-MS/MS	42	Apoptosis-related proteins	PYD and Card domain containing protein	Down
							DNA damage response	Proteasome activator complex subunit 2	Down
							Glycolysis	Phosphoglycerate mutase type B subunit	Down
							Xenobiotic metabolism and cellular defense	Glutathione S-transferase, Pi 2	Down
							Cytokine	Interleukin-12 p40 precursor	Up
							Proteins involved in cell growth, differentiation and signal trransduction	Nucleoside diphosphate kinases β isoform	Up
							Inflammatory factors	Myeloid-related protein	Up
							ATP transduction	ATP-citrate synthase	Up
							Redox regulation	Dismutase	Up
[49]	TNBS treated SD Rats			DRG	2D-MALDI- TOF-MS/MS	26	Xenobiotic metabolism and cellular defense	Glutathione S-transferase P (Gstp1)	Down
							Eliminating peroxides	Peroxiredoxin-1 (Prdx1)	Down
							1. Accelerate the folding of protein 2. Immunosuppression	Peptidyl-prolyl cis-trans isomerase A (Ppia)	Down
							1. Ion channel 2. Mitochondrial apoptosis	Voltage-dependent anion-selective channel protein 2 (Vdac2)	Down
							Cytoplasmic tetramerisation domain of voltage-gated K+ channel	similar to Potassium channel tetramerisation domain containing protein 12	Up
				Spinal cord		19	Xenobiotic metabolism and cellular defense	Glutathione S-transferase P (Gstp1)	Down
							1. Glycolytic enzyme 2. Autoantigen in many diseases	α-enolase (Eno1)	Down
							Immunity	Proteasome subunit α type-1 (Psma1)	Down

DRG: Dorsal root ganglia; TNBS: Trinitrobenzene sulfonic acid; CD: Crohn's disease; UC: Ulcerative colitis; DSS: Dextran sulfate sodium; NF: Nuclear factor.