Oligo-conjugated antibodies (Ab-seq) and massively parallel single cell sequencing reveal the high parameter correlation of protein and mRNA expression in individual immune cells.

Abstract

Abstract Single-Cell mRNA sequencing has enhanced our knowledge of the cell populations found in individual tissues or disease states. However, low correlation between mRNA and protein expression levels hinders our understanding of biology and disease. Traditional single cell protein assays are limited in the number of parameters that can be achieved within one experiment. Here we use oligo-conjugated antibodies (Ab-seq) in combination with massively parallel single cell mRNA sequencing on the BD Rhapsody™ platform to simultaneously measure the protein and mRNA content of individual human blood cells (PBMCs). To accomplish this, a 30+ parameter Ab-seq panel against immune relevant cell surface markers was paired with the BD Rhapsody™ Immune Response panel (a targeted gene expression panel consisting of 399 targets). The Multi-omics data from this single workflow experiment provides a measurement of both gene expression and protein expression. The digital measurements are rendered free of PCR bias through the use of the unique molecular indices (UMIs). Our results show that protein expression detected with Ab-seq is highly sensitive and specific. Protein expression patterns correlate well with results from flow cytometry data on the same samples. Ab-seq allowed the robust detection of expressed genes even when their cognate mRNA transcripts have low abundance. Certain markers cannot be easily distinguished at the mRNA level (i.e. isoforms CD45RA and CD45RO) but are easily distinguished at the protein level. Our study shows successful analysis of protein and mRNA expression data within a single workflow, and should enable the further elucidation single cells within different tissues, developmental time points, and disease states.