Discovery of Prognostic Biomarker Candidates of Lacunar Infarction by Quantitative Proteomics of Microvesicles Enriched Plasma

<div><p>Background</p><p>Lacunar infarction (LACI) is a subtype of acute ischemic stroke affecting around 25% of all ischemic stroke cases. Despite having an excellent recovery during acute phase, certain LACI patients have poor mid- to long-term prognosis due to the recurrence of vascular events or a decline in cognitive functions. Hence, blood-based biomarkers could be complementary prognostic and research tools.</p><p>Methods and Finding</p><p>Plasma was collected from forty five patients following a non-disabling LACI along with seventeen matched control subjects. The LACI patients were monitored prospectively for up to five years for the occurrence of adverse outcomes and grouped accordingly (i.e., LACI-no adverse outcome, LACI-recurrent vascular event, and LACI-cognitive decline without any recurrence of vascular events). Microvesicles-enriched fractions isolated from the pooled plasma of four groups were profiled by an iTRAQ-guided discovery approach to quantify the differential proteome. The data have been deposited to the ProteomeXchange with identifier PXD000748. Bioinformatics analysis and data mining revealed up-regulation of brain-specific proteins including myelin basic protein, proteins of coagulation cascade (e.g., fibrinogen alpha chain, fibrinogen beta chain) and focal adhesion (e.g., integrin alpha-IIb, talin-1, and filamin-A) while albumin was down-regulated in both groups of patients with adverse outcome.</p><p>Conclusion</p><p>This data set may offer important insight into the mechanisms of poor prognosis and provide candidate prognostic biomarkers for validation on larger cohort of individual LACI patients.</p></div

A) Histogram showing the iTRAQ ratios of selected proteins related to focal adhesion (ITGA2B, TLN1 and FLNA) and coagulation cascade (FGA, FGB and PLG).

<p>Demographically matched control group was used as the common denominator (i.e. 114) for comparing the three groups of LACI patients. The solid line indicates no change in regulation. The LACI groups with adverse outcome (recurrent vascular event, 116; cognitive decline, 117) had a differential signature in comparison with the LACI group with no adverse outcome (i.e. 115). Up-regulation of proteins related to focal adhesion and coagulation (FGA, FGB) at the baseline is predictive of poor outcome. *Denotes ratios with significant <i>p</i>-value (<0.05). B) Schematic diagram showing the interaction of various ligands of ITGA2B on platelet membrane and the probable involvement down-stream intracellular proteins (e.g. TLN1 and FLNA) in vascular dysfunction that may be responsible for poor prognosis. Aspirin partially blocks the integrin signaling as seen in the flowchart.</p

Schematic representation of the experimental design. ERLIC, electrostatic repulsion hydrophilic interaction chromatography.

<p>Schematic representation of the experimental design. ERLIC, electrostatic repulsion hydrophilic interaction chromatography.</p

Demographic Characteristics of the Patient Population Stratified by the Outcome Measures.

<p>All values are reported as: N(%), where N indicates the number of observations.</p>†<p>Values are expressed as: Mean (±standard deviation).</p

The List of Qualified and Regulated Proteome from Microvesicle-enriched Plasma <i>^a.</i>

a<p>The list contains quantitative information of the selected proteins from bias and background corrected iTRAQ data set. The denominator is the demographically matched control. Unused and %coverage are parameters related to the confident identification of proteins. This list contains 43 candidates qualified (out of 183) through the initial filters [i.e., unused prot score >3.0 and FDR = 1.1% (confident identification), <i>p</i>-value <0.05 (significantly different from 1) for at least one ratio]. The Significant ratios are indicated in bold. The uniport accession numbers of the ‘unreviewed’ proteins are indicated in <i>italics</i> form. The protein whose evidence is available only at the level of transcript is not provided with a gene symbol. The last column provides information about GO or pathway. CCC = complement and coagulation cascade, ECS = extracellular space, EIA = enzyme inhibitor activity, FA = focal adhesion, IIR = innate immune response, LT =  lipid transport, RTW = response to wounding. *Reported as microvesicle or exosome marker by independent studies.</p

A) Hierarchical clustering of the filtered list of proteins from microvesicle-enriched plasma.

<p>Log₂-transformed ratios (e.g. ln (115/114)) of each protein (row) were presented for all conditions (column). Pearson correlation was applied for the measurement of row and column distance. Globally normalized view was presented here. The color scale of the heat map ranges from saturated blue (value, −2.45) to saturated red (value, 2.19) in the natural logarithmic scale. The proteins were mainly clustered into two parts as shown by I (up-regulated in adverse outcome groups) and II (down-regulated in the adverse outcome groups). The pattern of regulation was similar between recurrent vascular event and cognitive decline group amid subtle differences in magnitudes. MBP and ALB were the two most regulated proteins. The protein names and accession numbers were taken from the uniprot protein database. The gene symbols are provided within brackets along with the protein name, wherever available. B) Technical validation of iTRAQ result by WB analysis of ALB on pooled lysates. ALB showed down-regulation in both LACI groups with adverse outcome, which is consistent with the iTRAQ result.</p

Pictures of a representative microvesicle pellet against different backgrounds.

<p>The loose orange-reddish hollow at the bottom of the tubes (shown by arrow) was obtained following ultracentrifugation (200 000 g, 2 h 15 min) of the microparticle-depleted pooled plasma.</p

Evaluation of the Effect of Trypsin Digestion Buffers on Artificial Deamidation

Nonenzymatic deamidation occurs readily under the condition of trypsin digestion, resulting in the identification of many artificial deamidation sites. To evaluate the effect of trypsin digestion buffers on artificial deamidation, we compared the three commonly used buffers Tris-HCl (pH 8), ammonium bicarbonate (ABC), and triethylammonium bicarbonate (TEAB), and ammonium acetate (pH 6), which was reported to reduce Asn deamidation. iTRAQ quantification on rat kidney tissue digested in these four buffers indicates that artificial Asn deamidation is produced in the order of ammonium acetate < Tris-HCl < ABC < TEAB, and Gln deamidation has no significant differences in all tested buffers. Label-free experiments show the same trend, while protein and unique peptide identification are comparable using these four buffers. To explain the differences of these four buffers in producing artificial Asn deamidation, we determined the half-life of Asn deamidation in these buffers using synthetic peptides containing -Asn-Gly- sequences. It is 51.4 ± 6.0 days in 50 mM of ammonium acetate (pH 6) at 37 °C, which is about 23, 104, and 137 times that in Tris-HCl, ABC, and TEAB buffers, respectively. In conclusion, ammonium acetate (pH 6) is more suitable than other tested buffers for characterizing endogenous deamidation and N-glycosylation

Quantitative Neuroproteomics of an <i>In Vivo</i> Rodent Model of Focal Cerebral Ischemia/Reperfusion Injury Reveals a Temporal Regulation of Novel Pathophysiological Molecular Markers

Cerebral ischemia or stroke, an acute neurological injury lacking an effective therapy, is the second leading cause of death globally. The unmet need in stroke research is to identify viable targets and to understand their interplay during the temporal evolution of ischemia/reperfusion (I/R) injury. Here we report a temporal signature of the ischemic hemisphere revealed by the isobaric tag for relative and absolute quantification (iTRAQ)-based 2D-LC–MS/MS strategy in an <i>in vivo</i> middle cerebral artery occlusion (MCAO) model of focal cerebral I/R injury. To recapitulate clinical stroke, two hours of MCAO was followed by 0, 4, and 24 h of reperfusion to capture ischemia with an acute and subacute durations of reperfusion injury. The subsequent iTRAQ experiment identified 2242 proteins from the ischemic hemisphere with <1.0% false discovery rate. Data mining revealed that (1) about 2.7% of detected proteins were temporally perturbed having an involvement in the energy metabolism (Pygb, Atp5b), glutamate excitotoxicity (Slc1a3, Glud1), neuro-inflammation (Tf, C3, Alb), and cerebral plasticity (Gfap, Vim, Gap43); (2) astrocytes participated actively in the neurometabolic coupling underlining the importance of a cerebro-protective rather than a neuro-protective approach; and (3) hyper-acute yet progressive opening of the blood brain barrier (BBB), accompanied by stimulation of an innate immune response and late activation of a regenerative response, which provides an extended therapeutic window for intervention. Several regulated proteins (Caskin1, Shank3, Kpnb1, Uchl1, Mtap6, Epb4.1l1, Apba1, and Ube1x) novel in the context of stroke were also discovered. In conclusion, our result supports a dynamic multitarget therapy rather than the traditional approach of a unilateral and sustained modulation of a single target to address the phasic regulation of an ischemic proteome

Additional file 1: Table S1. of An iTRAQ-based proteomic analysis reveals dysregulation of neocortical synaptopodin in Lewy body dementias

Complete information of the full list of the qualified proteins (Unused prot score > 2) obtained from the bias corrected iTRAQ data set. (XLSX 555 kb