Abstract
Background: There is increasing interest in the use of circulating cell-free RNA (cfRNA) in plasma as an analyte for diagnosing and monitoring disease. While it is known that cfRNA can also be isolated from urine, the diagnostic potential of urine cfRNA, particularly relative to plasma cfRNA, remains underexplored. Methods: Matched plasma and urine were collected from hematopoietic stem cell transplant (HSCT) recipients (n = 24), immune-checkpoint-inhibitor (ICI) recipients with or without acute kidney injury (AKI) (n = 46), and healthy volunteers (n = 5), yielding 297 samples. Unbiased cfRNA sequencing was performed, followed by comparison of molecular diversity, tissue and cellular origin, and diagnostic performance for systemic (HSCT) and renal (AKI) complications. Results: Urine and plasma cfRNA displayed distinct molecular composition and cellular origin across all groups. In HSCT, pronounced changes in plasma cfRNA were detected during the course of treatment, while urine cfRNA changes were minimal. Conversely, when comparing ICI recipients with and without AKI, cfRNA signatures indicative of disease and AKI etiology were observed in urine but not in plasma. These urine-derived signatures included injury markers and immune transcripts consistent with localized renal inflammation. Conclusions: This study reveals the distinct origin and diagnostic utility of plasma and urine cfRNA and suggests urine cfRNA is a promising analyte to monitor kidney injury, especially in the context of AKI following ICI treatment.