Rapid liquid biopsy assessment through gene profiling from the kidney biopsy transport medium: a technical validation and a proof-of-concept pilot study

Background: Rapid diagnosis is pivotal in kidney disease for timely and targeted treatment. Conventional microscopic and molecular assessments from biopsy tissues rely on extra sample processing (e.g., formalin-fixation, paraffin-embedding (FFPE)) or an extra biopsy core (e.g., Molecular Microscope Diagnostic System [MMDx]), making same-day diagnosis impractical. Therefore, we introduce a novel and freely accessible material, the biopsy transport medium (BTM), which can serve as a source of biomarkers with high potential and is promising for accelerating the assessment workflow. Methods: Biopsies were cut from tumor-free tissues obtained from nephrectomies to create BTM mimics for homogenization. We optimized the RNA extraction procedure from BTM by investigating crucial steps in the process. We measured the quantity and integrity of the RNA and different biomarkers derived from BTM through qPCR. Additionally, we performed the Banff Human Organ Transplant (B-HOT) panel on BTM from clinical biopsies using the NanoString nCounter platform as a proof-of-concept study. Results: Our results showed that the storage times ranging from 0.5 hours to 24 hours did not significantly affect RNA quality and yield. Differential gene expression analysis on allograft rejection BTM described specific profiles related to rejection. A significant correlation was observed between rejection-related transcripts and the corresponding Banff lesion scores. Conclusion: This study validated that the BTM can provide transcriptomic information relevant to the state of the kidney. The proof-of-concept study demonstrated that BTM has great potential for reflecting the status of the transplanted kidney. Tailored qPCR panels could allow for fast (same-day) molecular diagnosis.