Study design and transcriptional profiling of immune and neoplastic cells in the cHL microenvironment. (A) Outline of the scRNA-seq data set. Two data sets (Aoki et al10 and “this study”/WSI data set) were merged, and contain data from lymph nodes unaffected by lymphoma (reactive lymph nodes and nondiseased lymph nodes from deceased donors) highlighted in blue, and lymphoma-infiltrated lymph nodes highlighted in red. The numbers of cells are given in dark gray, and the number of donors in light gray. (B) UMAP plot of 243 753 cells from an integrated scRNA-seq data set, colored by cell type and organized by compartment (T cells, B cells, innate lymphocytes, myeloid, and stroma). (C) UMAP plot of 22 573 graph neighborhoods, colored by the differential abundance (log fold change) in lymphoma-affected or nonlymphoma-affected (deceased-donor lymph nodes or reactive lymph node) samples. Dot size is proportional to neighborhood size (median neighborhood size = 50 cells). (D) Volcano plot showing differentially expressed genes between microdissected GCs and HRSCs. Significant genes for HRSCs are indicated (|LFC| > 3; adjusted P value <.01). (E) Heatmap showing transcription factor (TF) regulon normalized enrichment scores for GCs vs HRSCs calculated with DoRothEA. (F) Graph indicating predicted interactions between genes (red, transcription factors; gray, other genes) differentially expressed in HRSCs. Edges drawn where an interaction is documented by OmniPath. (G) UMAP plot of 2727 myeloid cells colored by cell type. (H) Heatmap showing mean normalized expression levels (color) and fraction of cells expressing (dot size) markers of myeloid cell subsets. (I) Heatmap showing the proportion of each cell type derived from lymphoma and nonlymphoma samples.
