Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19

Dysregulated immune responses against the SARS-CoV-2 virus are instrumental in severe COVID-19. However, the immune signatures associated with immunopathology are poorly understood. Here we use multi-omics single-cell analysis to probe the dynamic immune responses in hospitalized patients with stable or progressive course of COVID-19, explore V(D)J repertoires, and assess the cellular effects of tocilizumab. Coordinated profiling of gene expression and cell lineage protein markers shows that S100Ahi/HLA-DRlo classical monocytes and activated LAG-3hi T cells are hallmarks of progressive disease and highlights the abnormal MHC-II/LAG-3 interaction on myeloid and T cells, respectively. We also find skewed T cell receptor repertories in expanded effector CD8+ clones, unmutated IGHG+ B cell clones, and mutated B cell clones with stable somatic hypermutation frequency over time. In conclusion, our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19.To perform sample demultiplexing, we used a hashing-based approach to deconvolute pooled CITE-Seq data. Specifically, each pooled CITE-Seq library (CITE_1 through CITE_6) was demultiplexed into its individual PBMC samples using unique hashing barcodes. For each CITE pool, the associated PBMC samples and their corresponding barcodes were identified and matched.The demultiplexing results are detailed as follows:CITE_1 was split into NS1A, NS1B, TS5A, TS5B, TP7A, TP7B,CITE_2 was split into the same set: NS1A, NS1B, TS5A, TS5B, TP7A, TP7B,CITE_3 was demultiplexed into NS0A, NS0B, TS2A, TS2B, TP6A,CITE_4 included NS0A, NS0B, TS2A, TS2B, TP6A, TP6B,CITE_5 included TS3A, TS3B, TS4A, TS4B, TP9B.CITE_6 included the same set: TS3A, TS3B, TS4A, TS4B, TP9B.Each sample was identified by its unique hashing barcode, allowing for accurate separation of individual samples from the pooled libraries.