Microscale combinatorial stimulation of human myeloid cells reveals inflammatory priming by viral ligands

Abstract

Cells sense a wide variety of signals and respond by adopting complex transcriptional states. Most single-cell profiling is carried out today at cellular baseline, blind to cells’ potential spectrum of functional responses. Exploring the space of cellular responses experimentally requires access to a large combinatorial perturbation space. Single-cell genomics coupled with multiplexing techniques provide a useful tool for characterizing cell states across several experimental conditions. However, current multiplexing strategies require programmatic handling of many samples in macroscale arrayed formats, precluding their application in large-scale combinatorial analysis. Here, we introduce StimDrop, a method that combines antibody-based cell barcoding with parallel droplet processing to automatically formulate cell population × stimulus combinations in a microfluidic device. We applied StimDrop to profile the effects of 512 sequential stimulation conditions on human dendritic cells. Our results demonstrate that priming with viral ligands potentiates hyperinflammatory responses to a second stimulus, and show transcriptional signatures consistent with this phenomenon in myeloid cells of patients with severe COVID-19.

Identification of In‐Droplet Multicellular Communities by Light‐Induced Combinatorial DNA Barcoding

“…Randomly encapsulating multiple cells inside microdroplets facilitates the dissection of heterogeneous cell populations into many isolated subcommunities; therefore, useful to break down the complexity and to assess individual cell-cell interaction events in a highly parallelized manner. [1] These systems have been employed in a wide range of applications, such as identifying novel antibiotics-producing microbes by screening multi-species bacterial interactions, [2] finding functional cells from a pool of engineered cells, [3] monitoring heterogenous single-cell interaction dynamics between immune and cancer cells, [4] conducting multiplex phenotypic screening of cell populations stimulated by drugs, [5] and screening genetic elements that regulate cellular crosstalk. [6] Despite these advances, it remains difficult to assess the outcomes of individual in-droplet subcommunity interactions by sequencing-based single-cell molecular profiling, as the identity of each subcommunity is lost when cells are released from droplets for pooled single-cell analysis.…”