Benchmarking transcriptome deconvolution methods for estimating tissue‐ and cell‐type‐specific extracellular vesicle abundances

Abstract Extracellular vesicles (EVs) contain cell‐derived lipids, proteins and RNAs; however, determining the tissue‐ and cell‐type‐specific EV abundances in body fluids remains a significant hurdle for our understanding of EV biology. While tissue‐ and cell‐type‐specific EV abundances can be estimated by matching the EV's transcriptome to a tissue's/cell type's expression signature using deconvolutional methods, a comparative assessment of deconvolution methods' performance on EV transcriptome data is currently lacking. We benchmarked 11 deconvolution methods using data from four cell lines and their EVs, in silico mixtures, 118 human plasma and 88 urine EVs. We identified deconvolution methods that estimated cell type‐specific abundances of pure and in silico mixed cell line‐derived EV samples with high accuracy. Using data from two urine EV cohorts with different EV isolation procedures, four deconvolution methods produced highly similar results. The three methods were also concordant in their tissue‐ and cell‐type‐specific plasma EV abundance estimates. We identified driving factors for deconvolution accuracy and highlighted the importance of implementing biological knowledge in creating the tissue/cell type signature. Overall, our analyses demonstrate that the deconvolution algorithms DWLS and CIBERSORTx produce highly similar and accurate estimates of tissue‐ and cell‐type‐specific EV abundances in biological fluids.