This shortlist provides ratios of plasma MEV-enriched protein abundances of lacunar infarction (LACI) patients with various outcome measures (NAO - no adverse outcome, RVE - recurrent vascular event, CD - cognitive decline) when compared to matched healthy control (HC) subjects. The data was generated by an 4-plex iTRAQ experiment on MEV-enriched pooled plama samples obtained from the above 4 groups of subjects.

Sample collection and clinical Information: The basline plasma samples of a total of 45 LACI patients were obtained from the cognitive sub-study of European Australasian Stroke Prevention in Reversible Ischemia Trial (ESPRIT-cog). Patients were eligible if they were within 6 months of a LACI. The control plasma was obtained from demographically matched 17 healthy subjects recruited at the same site. All patients underwent a neuropsychological test battery to determine their cognitive status to exclude any patients with dementia at the baseline. Data on various baseline risk factors were collected. All subjects were followed up annually for up to 5 yrs to monitor for the occurrence of any vascular event or for a change in the baseline cognitive status. For RVE group (n=11), the patients had stroke, peripheral artery disease, intracranial bleeds, or any cardiac ischemia (stable and unstable angina, myocardial infarctions) or death from any of the above. For CD group (n=15), the cognitive status of these patients declined from the respective baseline status during follow-up visits. For NAO group (n=19), patients did not suffer a recurrent vascular event or cognitive decline. The plasma samples were pooled group-wise before isolation of MEV-enriched samples.(PMID: 24752076)

Brief proteomics method: MEV-enriched samples were obtained by combining 12000g and 30000g fractions. The samples (83 µg/group) were redcued, alkylated and digested in-gel overnight with sequencing-grade modified trypsin (12.5 ng/µl). The peptides were labeled with 4-plex iTRAQ reagents. The labeled peptides were combined, desalted, and fractionated off-line into 34 fractions with Electrostatic Repulsion and Hydrophilic Interaction Chromatography. Protein mass spectrometry was performed on individual fractions with QSTAR Elite Hybrid MS. Analyst QS 2.0 software (Applied Biosystems) was used for the spectral data acquisition. (PMID: 26966714)

Data analysis: ProteinPilot Software 3.0 (Applied Biosystems) was used for the peak list generation, protein identification and quantification against the concatenated target-decoy Uniprot human database (191242 sequences). The false discovery rate (FDR) of peptide identification was set to be less than 1%. The dataset was corrected for bias and background in ProteinPilot. Protein identification score, number of 95% confident peptides detected for each protein, and %sequence coverage attained by 95% confident peptides are presented for each protein under identification parameters. A total of 146 out 573 proteins were significantly altered based on the dual criteria: |Log₂(ratio)|>0.58 and (-log₁₀(p-value))>1.30. Using additional filters such as favorable GO terms, direction of alterations, 63 proteins out of 146 are shortlisted as potential LACI biomarkers. The log ratios of altered proteins are color-coded: increased, Red; decreased, Blue.

GO term abbreviation: OGD, Oxygen Glucose Deprivation; C, Coagulation; E, Endothelium; V, Vesicle; In, Inflammation; Br, Brain-linked; Ox, Oxidation; Com, Complement

Reference: Datta, A., Chen, C., Gao, Y. G., and Sze, S. K. (2022) Int. J. Mol. Sci. 23, 11670

The website was created by Arnab Datta. Please contact Arnab Datta at arnabdattaju@gmail.com, arnabdatta@yenepoya.edu.in or Siu Kwan Sze at nsze@brocku.ca for comments or questions.

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LACI Biomarker Shortlist

Gene Symbol	Accession	Protein Name	Identification Parameters			NAO/HC		RVE/HC		CD/HC		GO Term
Gene Symbol	Accession	Protein Name	Protein Score	%Cov(95)	Peptides (95%)	Log₂(ratio)	P-Value	Log₂(ratio)	P-Value	Log₂(ratio)	P-Value	GO Term
FLII	Q13045	Protein flightless-1 homolog	4.6	1.9	2	-0.58	0.339	-2.11	0.040	-2.86	0.029
DYNC1H1	Q14204	Cytoplasmic dynein 1 heavy chain 1	6.9	0.4	2	-0.40	0.312	-0.98	0.050	-1.04	0.023	V, Br
AP2B1	P63010-2	Isoform 2 of AP-2 complex subunit beta	7.1	2.7	3	-0.57	0.230	-2.13	0.016	-1.01	0.140	E, V, Br
BCHE	P06276	Cholinesterase	7.2	7.0	3	-0.12	0.365	2.18	0.014	2.39	0.008
UBA52	P62987	Ubiquitin-60S ribosomal protein L40	7.4	29.7	3	-0.36	0.359	-1.54	0.036	-0.53	0.258	OGD, V
MYLK	Q15746-5	Isoform 4 of Myosin light chain kinase, smooth muscle	8.0	2.2	4	-0.47	0.413	-1.67	0.021	-1.77	0.027
CANX	P27824-2	Isoform 2 of Calnexin	8.3	8.0	4	-0.44	0.192	-2.39	0.016	-2.03	0.127	V, Br
KLKB1	H0YAC1	Plasma kallikrein (Fragment)	8.4	6.7	4	-0.58	0.258	-0.50	0.543	1.09	0.043	C
KIF2A	O00139-4	Isoform 4 of Kinesin-like protein KIF2A	8.4	6.5	4	-0.53	0.197	-1.99	0.017	-1.38	0.050	V
SLC2A1	P11166	Solute carrier family 2, facilitated glucose transporter member 1	10.6	13.2	6	1.04	0.079	-2.75	0.010	-1.00	0.128	OGD, Br
DIAPH1	A0A0G2JH68	Protein diaphanous homolog 1	10.9	5.0	5	-0.33	0.294	-2.10	0.001	-1.74	0.003	V
IQGAP2	Q13576	Ras GTPase-activating-like protein IQGAP2	10.9	1.8	3	0.25	0.051	-1.10	0.002	-2.02	0.001	V
PIGR	P01833	Polymeric immunoglobulin receptor	11.3	10.9	6	-0.88	0.482	1.14	0.062	1.70	0.026	In
PECAM1	P16284-6	Isoform Delta15 of Platelet endothelial cell adhesion molecule	11.6	10.0	5	-0.45	0.387	-1.21	0.035	-1.61	0.019	E, V
GANAB	Q14697	Neutral alpha-glucosidase AB	11.7	9.7	6	-0.53	0.162	-1.25	0.012	-1.50	0.005
PROS1	P07225	Vitamin K-dependent protein S	11.9	10.8	6	-0.13	0.375	1.16	0.029	1.24	0.027	C, V
HPR	A0A0A0MRD9	Haptoglobin-related protein	12.3	55.5	39	-2.50	0.283	1.04	0.167	2.50	0.040	In
HSP90B1	P14625	Endoplasmin	13.4	9.2	6	-0.68	0.099	-2.68	0.001	-1.59	0.004	OGD, V
ADD1	P35611-3	Isoform 3 of Alpha-adducin	13.4	9.8	6	0.39	0.141	-1.85	0.036	0.00	0.716	E, Br
FLOT2	E7EMK3	Flotillin-2	14.2	18.0	7	-0.35	0.373	-1.54	0.007	-0.62	0.111	V, Br
APOH	P02749	Beta-2-glycoprotein 1	14.5	28.1	12	-0.27	0.367	-2.76	0.002	-1.75	0.007	C, E
VASP	P50552	Vasodilator-stimulated phosphoprotein	15.0	19.7	7	-0.64	0.378	-3.36	0.002	-1.42	0.024
VTN	P04004	Vitronectin	17.5	20.9	13	-0.23	0.265	-1.82	0.003	-0.78	0.195	C, E, In
CAT	P04040	Catalase	17.6	22.8	8	0.61	0.046	-0.23	0.886	0.16	0.671	OGD, V, Ox
ATP5A1	P25705	ATP synthase subunit alpha, mitochondrial	18.3	21.2	9	-0.31	0.102	-1.81	0.005	-1.90	0.018
PZP	P20742	Pregnancy zone protein	18.6	16.8	126	-1.04	0.067	0.01	0.753	1.53	0.003
FCGBP	Q9Y6R7	IgGFc-binding protein	19.0	3.1	9	-1.37	0.038	1.37	0.017	2.48	0.000
HPX	P02790	Hemopexin	19.3	21.9	10	0.82	0.033	-0.90	0.022	0.11	0.706	V, In
TFRC	P02786	Transferrin receptor protein 1	19.5	14.2	9	-1.77	0.002	-0.27	0.298	0.01	0.870	V
PON1	P27169	Serum paraoxonase/arylesterase 1	20.0	39.7	11	0.82	0.005	-0.39	0.181	-0.29	0.200	Ox
KNG1	P01042-2	Isoform LMW of Kininogen-1	23.1	28.6	12	0.69	0.029	-1.02	0.018	0.24	0.473	C, I, In
APOL1	O14791	Apolipoprotein L1	25.3	34.7	14	-1.33	0.024	0.25	0.962	1.91	0.000	In
CD5L	O43866	CD5 antigen-like	25.6	41.2	16	-0.69	0.035	0.74	0.021	1.99	0.000	In
STOM	P27105	Erythrocyte band 7 integral membrane protein	27.0	50.0	20	-0.07	0.592	-0.82	0.008	-1.34	0.002	V
GP5	P40197	Platelet glycoprotein V	27.7	33.6	17	-0.45	0.078	-2.15	0.000	-1.90	0.000	C
C4BPA	P04003	C4b-binding protein alpha chain	28.1	28.3	19	-0.23	0.315	1.22	0.000	1.42	0.000	In
EPB42	P16452	Erythrocyte membrane protein band 4.2	29.5	19.0	16	0.96	0.000	-1.53	0.000	-0.72	0.132
MSN	P26038	Moesin	29.6	28.4	17	-0.17	0.353	-1.73	0.043	-0.44	0.269	C, E, V, In
ITGB3	P05106	Integrin beta-3	32.8	22.8	21	-0.56	0.002	-2.26	0.000	-2.13	0.000	C, E, Br
LGALS3BP	Q08380	Galectin-3-binding protein	35.9	34.4	23	-1.12	0.001	1.10	0.001	2.03	0.000
APOA1	P02647	Apolipoprotein A-I	39.2	56.9	23	-0.80	0.342	-1.40	0.017	0.96	0.005	E, V, In, Ox
EPB41	P11171-2	Isoform 2 of Protein 4.1	39.8	30.6	21	0.98	0.007	-2.48	0.001	-0.60	0.156	Br
APOE	P02649	Apolipoprotein E	40.1	68.4	25	0.13	0.438	-0.72	0.064	-0.94	0.037	C, E, V, In, Br
VCP	P55072	Transitional endoplasmic reticulum ATPase	43.9	36.6	21	-0.61	0.045	0.09	0.921	0.08	0.437	V, Br
SERPINA1	P01009	Alpha-1-antitrypsin	45.2	55.5	32	0.33	0.075	-1.47	0.000	-0.09	0.911	C, V
LPA	P08519	Apolipoprotein(a)	46.5	29.2	38	1.36	0.000	0.05	0.718	-0.48	0.492
F5	A0A0A0MRJ7	Coagulation factor V	47.3	11.9	22	-0.29	0.095	-2.13	0.000	-1.29	0.000	C, V
FCN3	O75636	Ficolin-3	48.3	64.9	87	0.27	0.520	-1.00	0.016	-0.93	0.020	Com
VWF	P04275	von Willebrand factor	48.7	9.7	28	-0.43	0.008	-1.09	0.000	1.49	0.000	C
IGHA1	P01876	Immunoglobulin heavy constant alpha 1	52.9	56.9	68	-0.85	0.388	-0.07	0.755	1.16	0.040
IGKC	P01834	Immunoglobulin kappa constant	54.5	91.6	123	-0.28	0.266	0.40	0.415	1.94	0.000
FGG	P02679	Fibrinogen gamma chain	69.2	61.6	99	-0.49	0.131	-2.56	0.000	0.43	0.302	C, E
HP	P00738	Haptoglobin	73.8	64.5	92	0.29	0.197	2.33	0.000	2.22	0.000	V, In
TF	P02787	Serotransferrin	75.2	52.6	57	0.58	0.003	-1.95	0.000	0.07	0.595	V
SLC4A1	P02730	Band 3 anion transport protein	98.1	41.8	99	1.05	0.000	-3.16	0.000	-1.05	0.000	C
FN1	P02751-15	Isoform 15 of Fibronectin	101.6	27.5	67	-0.85	0.010	0.76	0.000	1.54	0.000	C
FGA	P02671	Fibrinogen alpha chain	105.5	42.8	152	-0.19	0.044	-3.56	0.000	0.33	0.008	C, E, V, Br, In
FGB	P02675	Fibrinogen beta chain	110.1	81.9	118	-0.48	0.215	-3.48	0.000	0.28	0.238	C, E, V, Br, In
ANK1	P16157-14	Isoform Er13 of Ankyrin-1	145.5	45.4	110	0.94	0.000	-2.25	0.000	-0.41	0.001	V, Br
IGHM	P01871	Immunoglobulin heavy constant mu	192.7	69.1	390	-4.07	0.000	1.30	0.001	2.62	0.000
SPTB	P11277-2	Isoform 2 of Spectrin beta chain, erythrocytic	200.6	50.1	129	0.80	0.000	-3.20	0.000	-0.53	0.000	V
SPTA1	P02549	Spectrin alpha chain, erythrocytic 1	230.4	57.0	138	0.73	0.000	-2.96	0.000	-0.36	0.000	V, Br
ALB	P02768	Serum albumin	258.4	85.5	399	1.21	0.000	-2.75	0.000	0.05	0.487

Gene Symbol

Accession

Protein Name

Identification Parameters

NAO/HC

RVE/HC

CD/HC

GO Term

Protein Score

%Cov(95)

Peptides (95%)

Log₂(ratio)

P-Value

Log₂(ratio)

P-Value

Log₂(ratio)

P-Value