Fig. 1: Focal biallelic loss of TNFRSF17 in patient MM-1 after anti-BCMA CAR T therapy.

a, Pre-therapy circos plot of patient MM-1 based on WGS. The outer track runs clockwise from chromosome 1 to Y. The inner track shows CNVs (gains in light blue and losses in salmon). The lines inside the circle represent SVs (deletions in red, duplications in green, inversions in blue and interchromosomal translocations in black). b, A CN and SV plots showing the subclonal loss of TNFRSF17 mediated by a focal deletion (red line). c, ScCNV-seq heatmap comparing the CN changes in chromosomes 1–22 in pre-therapy (pre) versus post-relapse (post) CD138⁺ MM cells. d, Pre-therapy versus post-relapse CD138⁺ CN alteration at TNFRSF17 locus based on scCNV-seq. The barplot and table compare the percentages of cells harboring the CNVs in pre- versus post-CAR T/TCE relapse samples. e, Positron emission tomography scan of patient demonstrating left sacral ala relapse after anti-BCMA CAR T therapy. f, Uniform Manifold Approximation and Projection showing the distribution of CD138⁺ cells collected pre- and post-relapse using scRNA-seq. The cells are marked based on the gene expression of TNFRSF17 (expression in red and no expression in gray). g, Pre- versus post-relapse CD138⁺ BCMA protein expression (by monoclonal anti-BCMA antibody (clone 19F2)) using flow cytometry. h, CN alterations at MYC locus in pre- versus post-relapse CD138⁺ MM cells based on scCNV-seq.