Proteomics analysis of colon cancer progression

Saleem, Saira; Tariq, Sahrish; Aleem, Iffat; Sadr-ul Shaheed; Tahseen, Muhammad; Atiq, Aribah; Hassan, Sadia; Abu Bakar, Muhammad; Khattak, Shahid; Syed, Aamir Ali; Ahmad, Asad Hayat; Hussain, Mudassar; Yusuf, Muhammed Aasim; Sutton, Chris

doi:10.1186/s12014-019-9264-y

Clinical Proteomics

Table 3 (a) Functionally significant proteins increased in all stages of disease or in cancer stages (III, UII) (b) Functionally significant proteins decreased in all stages of disease or in both cancer stages (DDD, UDD). Significantly changed expression (± 1SD) in italic cells

From: Proteomics analysis of colon cancer progression

Accession	Description	Gene	MW (kDa)	Calc. pI	Mascot score	# Peptides Mascot	Coverage %	NAP/NC log2	CC NM/NC log2	CC M/NC log2
a
Cell cycle progression, proliferation, DNA folding
Q99459	Cell division cycle 5-like protein	CDC5L	92.194	8.18	41	2	3	3.82	2.18	3.98
Q8IX12	Cell division cycle and apoptosis regulator protein 1	CCAR1	132.739	5.76	106	3	3	2.16	2.16	2.42
P49321	Nuclear autoantigenic sperm protein	NASP	85.186	4.3	300	5	10	1.32	1.84	2.43
P39687	Acidic leucine-rich nuclear phosphoprotein 32 family member A	ANP32A	28.568	4.09	232	2	14	1.67	2.06	2.34
Q92688	Acidic leucine-rich nuclear phosphoprotein 32 family member B	ANP32B	28.770	4.06	367	2	14	2.15	2.76	3.09
P09429	High mobility group protein B1	HMGB1	24.878	5.74	1254	9	40	1.74	2.27	2.80
P26583	High mobility group protein B2	HMGB2	24.019	7.81	1066	7	25	1.71	2.09	2.89
O15347	High mobility group protein B3	HMGB3	22.965	8.37	450	4	28	1.43	1.74	2.52
P17096	High mobility group protein HMG-I/HMG-Y	HMGA1	11.669	10.32	213	2	33	3.78	3.65	3.85
Q969G3	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1	SMARCE1	46.621	4.88	56	1	3	1.80	2.37	3.16
Matrix degradation
P83110	Serine protease HTRA3	HTRA3	48.577	7.09	61	1	3	1.31	1.74	2.83
P80188	Neutrophil gelatinase-associated lipocalin	LCN2	22.574	8.91	417	3	23	1.34	2.14	3.18
P24158	Myeloblastin	PRTN3	27.789	8.35	658	4	28	1.26	3.79	3.50
P02788	Lactotransferrin	LTF	78.132	8.12	3542	30	49	1.72	2.52	4.19
P14780	Matrix metalloproteinase-9	MMP9	78.408	6.06	358	6	10	0.68	3.38	3.69
O75173	A disintegrin and metalloproteinase with thrombospondin motifs 4	ADAMTS4	90.139	7.85	26	1	1	0.60	1.90	2.90
P08246	Neutrophil elastase	ELANE	28.500	9.35	665	8	42	− 0.03	1.87	2.82
Cytoskeletal remodelling
Q8NF91	Nesprin-1	SYNE1	1010.456	5.53	41	3	0	− 1.00	1.80	3.14
Q16658	Fascin	FSCN1	54.496	7.24	339	6	14	− 0.37	1.84	3.24
P59998	Actin-related protein 2/3 complex subunit 4	ARPC5	19.654	8.43	89	2	10	− 0.23	1.61	2.54
P55008	Allograft inflammatory factor 1	AIF1	16.693	6.24	566	1	14	− 0.19	2.04	2.69
P05109	Protein S100-A8	S100A8	10.828	7.03	2582	8	72	0.00	3.76	2.38
P06702	Protein S100-A9	S100A9	13.234	6.13	6645	7	63	0.19	4.05	2.45
P13796	Plastin-2	LCP1	70.244	5.43	1803	15	40	0.27	2.68	2.07
P40121	Macrophage-capping protein	CAPG	38.474	6.19	1382	9	35	0.33	2.00	3.07
Q96SB3	Neurabin-2	PPP1R9B	89.138	4.97	35	1	1	0.69	1.73	3.42
Q99439	Calponin-2	CNN2	33.675	7.33	668	5	24	0.75	2.06	2.46
Q12792	Twinfilin-1	TWF1	40.258	6.96	40	2	12	0.80	2.04	2.35
Q9UQB8	Brain-specific angiogenesis inhibitor 1-associated protein 2	BAIAP2	60.830	8.9	73	1	3	0.89	2.41	2.46
Q13177	Serine/threonine-protein kinase PAK 2	PAK2	58.006	5.96	173	3	16	1.09	1.88	2.23
Immunity/inflammation
P02671	Fibrinogen alpha chai	FGA	94.914	6.01	2948	17	19	− 0.57	2.36	3.84
P02675	Fibrinogen beta chain	FGB	55.892	8.27	4950	28	61	− 0.95	2.19	3.20
P02679	Fibrinogen gamma chain	FGG	51.479	5.62	2304	18	49	− 0.96	2.66	3.28
P59665	Neutrophil defensin 1	DEFA1	10.194	6.99	358	2	19	0.34	2.01	2.54
P12838	Neutrophil defensin 4	DEFA4	10.497	8.02	54	1	18	1.19	2.21	2.44
b
Extracellular matrix
Q96P44	Collagen alpha-1(XXI) chain	COL21A1	99.307	8.32	76	1	1	− 3.27	− 5.81	− 6.30
P02462	Collagen alpha-1(IV) chain	COL4A1	160.514	8.28	1483	6	5	− 2.70	− 2.71	− 2.94
P39060	Collagen alpha-1(XVIII) chain	COL18A1	178.077	6.01	395	3	2	− 2.00	− 3.09	− 2.75
P08572	Collagen alpha-2(IV) chain	COL4A2	167.449	8.66	1983	13	12	− 2.18	− 2.71	− 2.80
P08123	Collagen alpha-2(I) chain	COL1A2	129.235	8.95	2714	9	8	− 2.62	− 2.44	− 2.56
P02452	Collagen alpha-1(I) chain	COL1A1	138.857	5.80	1814	9	9	− 2.92	− 1.95	− 2.37
Q05707	Collagen alpha-1(XIV) chain	COL14A1	193.394	5.30	894	20	16	− 2.52	− 2.55	− 2.16
Q14031	Collagen alpha-6(IV) chain	COL4A6	163.704	9.20	135	1	1	− 0.61	− 2.46	− 3.94
P12111	Collagen alpha-3(VI) chain	COL6A3	343.457	6.68	21068	100	41	− 1.81	− 2.20	− 2.44
P12110	Collagen alpha-2(VI) chain	COL6A2	108.512	6.21	5018	24	29	− 2.15	− 1.85	− 1.99
P12109	Collagen alpha-1(VI) chain	COL6A1	108.462	5.43	6769	25	37	− 1.87	− 2.00	− 2.09
P20908	Collagen alpha-1(V) chain	COL5A1	183.447	5.06	29	2	2	− 0.18	− 2.20	− 2.24
Q16363	Laminin subunit alpha-4	LAMA4	202.397	6.28	475	12	10	− 2.72	− 2.05	− 1.98
O15230	Laminin subunit alpha-5	LAMA5	399.479	7.02	1735	28	11	− 2.89	− 3.34	− 2.30
P55268	Laminin subunit beta-2	LAMB2	195.854	6.52	1451	27	23	− 2.88	− 3.28	− 2.42
P13727	Bone marrow proteoglycan	PRG2	25.189	6.76	637	5	30	− 1.37	− 2.85	− 4.55
Q6UVK1	Chondroitin sulfate proteoglycan 4	CSPG4	250.382	5.47	134	2	2	− 1.14	− 2.98	− 2.95
Q9Y2Y8	Proteoglycan 3	PRG3	25.389	4.81	222	3	16	− 0.33	− 2.93	− 2.41
P07585	Decorin 1	DCN	39.722	8.54	1574	13	51	− 2.66	− 4.53	− 3.85
P21810	Biglycan	BGN	41.628	7.52	1834	11	46	− 1.73	− 1.91	− 1.89
P14543	Nidogen-1	NID1	136.291	5.29	904	15	17	− 2.65	− 2.98	− 2.43
Q14112	Nidogen-2	NID2	151.158	5.29	640	11	13	− 1.56	− 2.67	− 2.23
P35613	Basigin	BSG	42.174	5.66	319	5	18	− 1.71	− 2.02	− 2.22
Cell adhesion and plasma membrane integrity
P08648	Integrin alpha-5	ITGA5	114.465	5.77	678	10	13	− 2.26	− 3.08	− 3.34
P05556	Integrin beta-1	ITGB1	88.357	5.39	3088	16	25	− 1.21	− 2.18	− 2.10
P18084	Integrin beta-5	ITGB5	87.996	6.06	225	3	4	− 1.28	− 2.18	− 2.03
P23229	Integrin alpha-6	ITGA6	126.526	6.61	1739	23	25	0.18	− 2.21	− 1.95
P27216	Annexin A13	ANXA13	35.393	5.60	251	3	9	− 1.57	− 2.85	− 3.33
P20073	Annexin A7	ANXA7	52.706	5.68	225	3	8	− 1.69	− 2.60	− 2.85
P08133	Annexin A6	ANXA6	75.826	5.60	3275	30	50	− 2.02	− 1.96	− 2.32
P13688	Carcinoembryonic antigen-related cell adhesion molecule 1	CEACAM1	57.525	5.97	148	2	6	− 2.64	− 4.05	− 3.02
Q14002	Carcinoembryonic antigen-related cell adhesion molecule 7	CEACAM7	29.361	5.54	335	2	12	− 2.05	− 3.26	− 3.91
P09326	CD48 antigen	CD48	27.665	8.07	90	2	10	− 1.39	− 4.10	− 4.48
P13987	CD59 glycoprotein	CD59	14.168	6.48	428	4	25	− 0.88	− 1.78	− 1.93
P08962	CD63 antigen	CD63	25.619	7.81	74	1	9	− 0.48	− 2.92	− 3.25
P60033	CD81 antigen	CD81	25.792	5.29	184	3	25	− 1.27	− 2.25	− 2.68
P21926	CD9 antigen	CD9	25.399	7.15	475	3	21	0.09	− 1.83	− 2.53
Q99795	Cell surface A33 antigen	GPA33	35.609	4.93	694	9	37	− 0.72	− 2.78	− 3.35
P04233	HLA class II histocompatibility antigen gamma chain	CD74	33.494	8.44	296	3	9	− 0.17	− 1.97	− 2.60
P28907	ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1	CD38	34.306	7.66	302	6	23	− 0.21	− 2.11	− 2.29
P04899	Guanine nucleotide-binding protein G(i) subunit alpha-2	GNA12	40.425	5.54	1216	10	36	− 1.55	− 3.17	− 3.09
Q9UBI6	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-12	GNG12	8.001	8.97	31	1	26	− 0.11	− 2.76	− 5.24
P62873	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	GNB1	37.353	6.00	761	6	26	− 0.76	− 3.82	− 4.44
P62879	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2	GNB2	37.307	6.00	527	6	26	− 1.01	− 3.37	− 4.56
P29992	Guanine nucleotide-binding protein subunit alpha-11	GNA11	42.097	5.69	364	3	15	− 1.60	− 1.79	− 1.97
Q14344	Guanine nucleotide-binding protein subunit alpha-13	GNA13	44.022	8.00	525	3	7	− 1.43	− 2.28	− 3.42
Q9HAV0	Guanine nucleotide-binding protein subunit beta-4	GNB4	37.543	6.00	116	3	13	− 2.70	− 4.18	− 4.28
Excretion, transport of metabolites and modification of xenobiotics
O75795	UDP-glucuronosyltransferase 2B17	UGT2B17	61.055	8.54	895	8	14	− 6.21	− 4.49	− 5.67
P40879	Chloride anion exchanger	SLC26A3	84.451	8.69	91	2	3	− 4.01	− 4.36	− 4.89
Q6UWM9	UDP-glucuronosyltransferase	2A3	UGT2A3	60.215	7.96	234	4	10	− 3.83	− 6.25
Q14CN2	Calcium-activated chloride channel regulator	4	CLCA4	PE=1	1S0V1=.219	5.47	274	5	6	− 3.59
P54289	Voltage-dependent calcium channel subunit alpha-2/delta-1	CACNA2D1	124.49	5.27	59	2	3	− 2.55	− 4.72	− 4.82
P50443	Sulfate transporter	SLC26A2	81.609	8.38	102	2	4	− 2.16	− 2.58	− 3.90
Q96KA5	Cleft lip and palate transmembrane protein 1-like protein	CLPTM1L	62.189	8.56	68	3	8	− 2.13	− 3.85	− 3.23
O15438	Canalicular multispecific organic anion transporter 2	ABCC3	169.234	7.20	46	1	1	− 1.95	− 2.72	− 2.90
Q15041	ADP-ribosylation factor-like protein 6-interacting protein 1	ARL6IP1	23.347	9.32	27	1	5	− 1.69	− 2.03	− 2.63
O14936	Periphera plasma membrane protein CASK	CASK	105.056	6.43	28	1	1	− 1.58	− 1.97	− 2.55
P20020	Plasma membrane calcium-transporting ATPase 1	ATP2B1	138.668	6.04	123	5	4	− 1.38	− 2.29	− 3.75
P16662	UDP-glucuronosyltransferase 2B7	UGT2B7	60.655	8.31	618	3	7	− 1.36	− 3.71	− 4.13
P10301	Ras-related protein R-Ras	RRAS	23.466	6.93	217	3	15	− 1.32	− 3.18	− 3.27
Q8NE86	Calcium uniporter protein, mitochondrial	MCU	39.842	8.65	181	5	16	− 1.32	− 2.48	− 3.15
Q6UWW8	Carboxylesterase 3	CES3	62.242	5.62	137	3	10	− 0.46	− 1.80	− 1.91
P23141	Liver carboxylesterase 1	CES1	62.481	6.60	81	2	4	− 2.12	− 1.78	− 1.90
P50225	Sulfotransferase 1A1	SULT1A1	34.143	6.62	187	1	13	− 3.21	− 3.38	− 4.38
P0DMN0	Sulfotransferase 1A4	SULT1A4	34.174	6.01	240	2	17	− 0.97	− 1.25	− 3.23
P07099	Epoxide hydrolase 1	EPHX1	52.915	7.25	280	6	17	− 2.41	− 2.29	− 2.42
P37059	Estradiol 17-beta-dehydrogenase 2	HSD17B2	42.757	8.50	57	1	4	− 2.52	− 3.78	− 3.76
Q92506	Estradiol 17-beta-dehydrogenase 8	HSD17B8	26.957	6.54	402	4	20	0.57	− 1.91	− 2.14
P80365	Corticosteroid 11-beta-dehydrogenase isozyme 2	HSD11B2	44.098	9.28	453	6	22	− 2.35	− 3.66	− 4.13

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