22269124

<strong>Objective: </strong>To analyse the proteomic profile of thrombi in ischemic stroke (IS) patients, in order to gain insights into disease pathogenesis. <strong>Approach and results: </strong>Thrombi from an exploratory cohort of stroke patients were obtained by thrombectomy and analysed by SWATH-MS. Unsupervised k-means clustering analysis was performed to stratify stroke patients. The proteomic profile was associated with both, the neurological function (NIHSS) and the cerebral involvement (ASPECTS) prior to thrombectomy and the clinical status of patients at 3 months using the modified Rankin scale (mRS90). In an independent cohort of 210 stroke patients, the potential role of neutrophils in stroke severity was interrogated. Proteomic analysis identified 580 proteins in thrombi, which were stratified in 4 groups: haemostasis; proteasome and neurological diseases; structural proteins; and innate immune system and neutrophils. The thrombus proteome identified 3 clusters of patients with distinctive severity, prognosis and aetiology of the stroke. A protein signature clearly distinguished atherothrombotic and cardioembolic strokes. Several proteins were significantly correlated with the severity of the stroke (NIHSS and ASPECTS). Functional proteomic analysis highlighted the prominent role of neutrophils in the stroke severity. This was in line with the association of neutrophils activation markers and count with NIHSS, ASPECTS and mRS90. <strong>Conclusions: </strong>The use of the SWATH-MS in thrombi from IS patients has provided new insights of pathways and players involved in its aetiology, severity and prognosis. The prominent role of the innate immune system identified might pave the way for the development of new biomarkers and therapeutic approaches in this disease.