TRACE-seq: A transgenic system for unbiased loading of mRNA into extracellular vesicles allowing non-invasive transcriptome profiling of living cells

Changes in gene expression due to cell heterogeneity and response to stressors in specific microenvironments remains poorly understood. Current methodologies that seek to interrogate gene expression at a molecular level require sampling of cellular transcriptome and therefore lysis of the cell preventing serial analysis of cellular transcriptome. To address this area of unmet need, we have recently developed a new technology allowing transcriptomic analysis over time without cellular destruction. Our novel method, TRACE-seq (TRanscriptomic Analysis Captured in Extracellular vesicles using sequencing), is characterized by a cell-type specific transgene expression. It provides data on a representative part of the cell transcriptome inside extracellular vesicles. Thus, the transcriptome of cells expressing TRACE can be followed over time in a non-destructive manner, which is a powerful tool for many fields of fundamental and translational biology research. HEK cells were transfected with 4EC1 vectors (eGFP-EIF4E-C-YTHDF1/GBP1-CD9) and exposed to normoxia or hypoxia conditions. The cellular RNAs and extracellular RNAs were sequenced and analyzed.