Protein- and sequencing-based massively parallel single-cell approaches to immune profiling asthma-specific cell subtypes and related gene expression biomarkers

Abstract

Abstract We implemented the BD Rhapsody Single-Cell Analysis System to assess cellular heterogeneity present in twins by capturing and sequencing over 40000 single cells across 10 samples from 5 twins patients with asthma or without asthma using oligos-conjugated antibodies and the whole blood immune targeted gene panel that utilizes multiplex PCR for detection of over 500 genes for immune cells subtyping, immunophenotyping, cell-type identification and markers correlated with stimulations. A combinatorial library of beads bearing cell- and molecular-barcoding capture probes is used to uniquely label transcripts and reconstruct the digital gene expression profile of thousands of individual cells in a single experiment without the need for robotics or automation. We demonstrate the ability of the BD Rhapsody targeted panel to distinguish six different cell types and 18 distinct gene-expression biomarkers, including CLEC4E, CSF2, IL1RN, TPSAB1, CCL19, CCL22, CXCL2, LAMP3, SPP1, and VMO etc.. The HLA-DRA, HLA-DQB1, SPP1, and IL1RN had allelic polymorphism related to asthma. The BD Rhapsody targeted panel yields more sequencing depth with much fewer (<2%) sequencing reads per cell. The measurement of specific proteins and transcripts in individual cells is critical for understanding the role of cellular diversity in development, health, and disease.