A combined approach for single-cell mRNA and intracellular protein expression analysis

Combined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation. Here, the authors present SPARC, a scalable approach for simultaneously measuring mRNA expression levels and targeted intracellular protein levels in single cells. They use SPARC to measure dynamic expression changes in human cells during neuronal differentiation and show that mRNA levels are poor predictors of protein abundances and activity in individual cells, indicating that the measurements are complementary.

Automated summary

The SPARC method combines single-cell RNA sequencing with proximity extension assays to measure global mRNA and 89 intracellular proteins simultaneously in individual cells. Results show that mRNA expression does not accurately reflect protein abundance, with protein levels of transcription factors better predicting downstream effects. Overall, protein expression variation is lower than mRNA variation in single cells, but relative protein variation does not correlate with mRNA level.