Abstract Body: Introduction: Both histological and transcriptomic analyses of acute ischemic stroke (AIS) clots have identified features associated with mechanical thrombectomy (MT) outcome. However, few studies have explored how fluorescence histology and mRNA sequencing from the same clot can pinpoint specific biological phenomena associated with MT failure.

Hypothesis: Joint analysis of paired clot immunofluorescence histology and mRNA sequencing will identify Neutrophil Extracellular Trap (NET) enrichment as a biomarker of MT first pass (FP) outcome.

Methods: We performed paired histological and transcriptomic analysis of 32 stroke clots retrieved by MT (n=16 each of FP success and failure). Immunofluorescence histology was completed by co-staining 4µm clot tissue sections with antibodies against NET components (neutrophil elastase [ELANE], citrullinated histone [CitHis]) and super resolution imaging with instant structured illumination microscopy (ISIM) at 100X magnification. Differentially expressed genes (DEGs) were identified between transcriptomes of FP success and failure using the criteria of logFC≥1.5 and q<0.05. Principal component analysis (PCA) and Ingenuity Pathway Analysis (IPA) were completed to evaluate how well DEGs separated clots based on FP outcome and to identify enriched biological processes.

Results: 44 DEGs were identified, most of which were downregulated in clots with successful FP. Expression of DEGs was able to separate clots by FP outcome. The NET signaling pathway was identified as the most enriched biological process in the FP failure group, with related genes downregulated in the FP success group. NETs were detected in clots with FP failure.

Conclusion: Our results suggest that future multi-omic models, upon integration with pre-MT CT radiomics, can be developed to inform thrombolytic therapy and device selection, as well as predict FP outcome.