318 Profiling Long RNA Transcriptome From Circulating Extracellular Vesicles in Subarachnoid Hemorrhage for Biomarker Discovery

Abstract

INTRODUCTION: Aneurysmal subarachnoid hemorrhage (aSAH) is associated with a high mortality rate and permanent neurological deficits following acute brain injury. Previous studies have aimed at investigating CNS specific biomarkers that can predict the outcomes following aSAH. Liquid biopsy represents a promising minimally invasive approach for biomarker discovery using biofluids (plasma, CSF). METHODS: CSF was collected from patients (n = 10) during in-hospital stay at multiple time points via the external ventricular drain and EV RNA was sequenced using Oxford Nanopore Technologies. RESULTS: We detected different biotypes in EV RNA with minimal rRNA contamination (protein coding; 58.4%, pseudogene; 23.1%, LncRNA; 10%, rRNA; 1.7%). This is the first study reporting presence of long (>500 bp) RNA transcripts in CSF derived EVs. Approximately, 80% of the sequenced reads were up to 500 bp long and 20% reads 500-10,000 bp long. Principal Component Analysis demonstrated distinct clustering of samples based on location (anterior vs. posterior circulation) and type of aneurysm (saccular, dissecting, bilobed). A set of protein coding genes (S100A9, EEF1A1, SCARNA1, DMTN) were found to be differentially enriched in patients who developed cerebral vasospasm (n = 6). Furthermore, for each patient there was a unique population of biomarkers upregulated in acute (HBB, COX2) vs. chronic (SEPTIN7, PDK4) immune response following aSAH. Preliminary findings reveal potential candidate biomarkers providing insight into the pathogenesis and prognosis. CONCLUSIONS: There is an unmet need for inclusion of diagnostic and predictive biomarkers in clinical management of aSAH to decrease the overall mortality. In this study, we overcame challenges of analyzing low input RNA using a sensitive and optimized sequencing platform. Validation and testing in a larger study population offers new opportunities for biomarker discovery.