Single-cell transcriptome analysis corroborate reduced inflammatory activity under vemurafenib. (A) Single-cell RNA sequencing (scRNA-seq) was performed on one peripheral blood sample and one bone marrow aspirate before and during therapy, respectively. (B) Percentage of mutated BRAF in fluorescence-activated cell sorted bone marrow cells at diagnosis and during therapy. (C) Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) visualization showing all the cells detected in the scRNA-seq dataset. Following quality control, the transcriptome of bone marrow aspirates at diagnosis (day −6; 5,031 cells) and during therapy (day 70; 6,444 cells), as well as peripheral blood samples at diagnosis (day −2; 7,384 cells) and during therapy (day 120; 9,269 cells), were analyzed. Cell types were annotated by mapping the cells on a reference dataset using the Azimuth pipeline and indicated in different colors. (D) Dot plot showing the expression of the top 3 expressed genes by cell types. Normalized mean expression across samples is indicated by color and the percentage of cells expressing the gene (>0) per cluster is indicated by dot size. (E) GSEA of genes downregulated during vemurafenib therapy compared with diagnosis. The top 3 Gene Ontology pathways ordered by normalized enrichment score (NES) are shown. *P < .1; **P < .05; ***P < .001. (F) Expression levels of AREG, IL1B, and CXCL8 in 11 475 bone marrow cells at time of diagnosis (red) and during vemurafenib-induced clinical remission (green). (G) Fold change (natural log) and P values (MAST test) of genes expressed in hematopoietic stem cells (HSCs) from bone marrow samples at diagnosis and during vemurafenib-induced clinical remission.