Mapping immune cellular landscapes and vaccine responses across a spectrum of health and immunodeficiency with single-cell RNA-seq.

Immune responses to infection or vaccination exhibit diversity between individuals that can be shaped by differences in their immune cell landscapes and the signalling, transcriptional, and genetic mechanisms that coordinate immune cell function. Specific antibody deficiency (SAD) and common variable immunodeficiency (CVID) are common forms of predominantly antibody deficiencies that result in poor responses to vaccination. While molecular and cellular causes of the immune dysfunction and poor vaccination responses for individuals with CVID have been reported, immune cell or molecular defects have not yet been identified in SAD. Here, we have used single-cell multi-omics to define the cellular landscapes, transcriptional states, adaptive immune repertoires and protein expression of patients with SAD and CVID before (day 0) and after (day 7) polysaccharide vaccination. PBMC samples were stained with Hash Tag Oligonucleotides (HTOs) and a panel of 130 Antibody-Derived Tags (ADTs) using TotalSeqTM antibodies (BioLegend). All 60 samples were then pooled and split into 5 batches (12 samples each) prior to 10X Genomics Chromium single-cell 5′ reagent kit v3 according to manufacturer’s protocol. Libraries were then sequenced on a NovaSeq X Plus (PE150). Cellranger multi and cellranger vdj (v8.0.1; 10x Genomics) were respectively used to align the CITE-seq and VDJ-seq libraries to the hs1 reference genome and to generate the cell barcode-gene UMI count matrices.