Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures

The human immune system consists of many specialized cell subsets that simultaneously carry out a diverse range of functions using overlapping pathways and signals. Subset-specific immune profiling can resolve immune activity in autoimmune disease, cancer immunity, and infectious disease that may not be discoverable or detectable in analyses of crude blood samples. Here, we present a low-input microfluidic system for sorting immune cells into subsets and profiling their cellular states by gene expression analysis using full-length RNA-seq. We validate the device’s technical performance by benchmarking its subset enrichment and genomic profiling performance against gold standard benchtop protocols and make the added value of subset-resolved profiling over crude sample analysis clear through in vitro experiments that show subset-specific stimulated responses. Our results show that even the canonical cytokine, IFN-α, can elicit opposing responses across different subsets. Finally, we show the scalability of our device by profiling four immune cell subsets in blood from systemic lupus erythematosus (SLE) patients and matched controls enrolled in a clinical study. Subset-specific expression profiling of PBMCs from healthy and SLE individuals. Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.