Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_RNA_with_blocking]
Enhancers and transcription factors (TFs) are crucial in regulating cellular processes, including disease-associated cell states. Current technologies to study these elements in gene regulatory mechanisms lack multiplexing capability and scalability. Here, we present SUM-seq, a cost-effective, scalable Single-cell Ultra-high-throughput Multiomic sequencing method for co-assaying chromatin accessibility and gene expression in single nuclei - enabling experiments at the million cell and hundreds of samples scale. SUM-seq outperforms current high-throughput single cell methods in sensitivity. We applied SUM-seq to dissect the gene regulatory mechanisms governing macrophage polarization, and explored their link to traits from genome-wide association studies (GWAS). Our analyses confirmed known TFs orchestrating M1 and M2 macrophage programs, unveiled new regulators, and suggested extensive enhancer rewiring. Integration with GWAS data further pinpointed the impact of specific TFs on a set of immune traits. Notably, enhancers regulated by the STAT1/STAT2/IRF9 (ISGF3) complex were enriched for rheumatoid arthritis (RA)-associated genetic variants, with the strongest link pointing to the CD40 gene, an emerging drug target for RA. This highlights the potential of SUM-seq for dissecting molecular disease mechanisms. In summary, SUM-seq provides a simple workflow for cost-effective, scalable single-cell ultra-high-throughput multiomic sequencing. It is particularly adept at elucidating complex gene regulatory networks in cell differentiation, response to perturbations, and disease contexts. Overall design: To optimise and evaluate performance and quality, we performed SUM-seq on an equal mixture of human leukemia (K562) and mouse fibroblast (NIH-3T3) cell lines