Systemic effects of ipilimumab. (A) Peripheral blood T-cell subsets in patients with myeloid (n = 14) and nonmyeloid (n = 6) disease pre-ipi and after 1 (C2D1) or 3 (C4D1) cycles of ipilimumab (post-ipi) quantified using flow cytometry as percentage of CD4⁺ or CD8⁺ T cells. (B) MDS plot calculated from CyTOF data of peripheral blood T cells of 10 NR patients pre-ipi (baseline, n = 10), 1 cycle post-ipi (C2D1, n = 10), or a later timepoint (follow-up, n = 8). Numbers next to dots refer to the patient identifiers used throughout the study (supplemental Tables 4-7). (C) Mean metal intensity (CyTOF) on CD4⁺ and CD8⁺ T cells pre-ipi (blue) or 1 cycle post-ipi (yellow) from samples shown in panel B. (D) Frequency of CDR3α and CDR3β sequences in peripheral blood pre-ipi (baseline) and post-ipi (C2D1) (n = 572 017; TCR repertoire sequencing). Dynamic CDR3 sequences with significant changes in abundance (adjusted P value < .01) in purple (expanded, novel = not detectable pre-ipi) or green (contracted, disappeared = not detectable post-ipi). (E) Percentage of CDR3 sequences from disease biopsies detectable in peripheral blood pre-ipi and post-ipi. (F) Absolute number of dynamic CDR3 sequences in patients with response to ipilimumab (CR/TR) (blue, n = 4) and NR (red, n = 5). (G) Differential protein expression post-ipi in patients with response (n = 4) vs patients without response (n = 8) to ipilimumab measured with proximity extension assay (PEA, Olink). (H) Heatmap of protein expression measured with PEA in NR pre-ipi (n = 8), NR post-ipi (n = 16), CR/TR pre-ipi (n = 4), CR/TR post-ipi (n = 8). C2D1/C4D1, second/fourth cycle of ipilimumab; EM, effector memory T cell; MDS, multidimensional scaling; MMI, mean metal intensity; naive, naive T cell; PB, peripheral blood.