Response to ipilimumab is characterized by transcriptional evidence of T-cell infiltration and activation. (A) RNA sequencing on FFPE disease-site biopsies (♦, n = 33) from 3 patients with CR (17, 21, 26; dark blue), 3 patients with TR (6, 14, 28; light blue) and 7 patients with NR (5, 11, 22, 24, 29, 31, 33; red) pre-ipi or post-ipi ipilimumab treatment. Disease sites: bone marrow (light), extramedullary (dark), or isolated skin (white). Peripheral blood samples (●, n = 28) used for TCR repertoire sequencing. (B) DGEA between 4 site-matched biopsies from CR patients (top) and between unmatched biopsies from NR patients pre- (n = 7) vs post-ipi (n = 8) (bottom). Genes that are part of the Gene Ontology term “leukocyte activation” are labeled and those associated with T-cell activation are highlighted. (C) Gene ontology enrichment analysis of the differentially expressed genes. (D) PCA based on expression of the differentially expressed genes. Biopsies from all CR pre-ipi (n = 4, gray) and post-ipi (n = 7, blue), NR pre-ipi (n = 7, salmon), and post-ipi (n = 8, red) samples, and biopsies from sites of GVHD or immune-related toxicities (n = 9, black). (E,F) Cell type abundance estimation of CD8⁺ T cells with (E) CIBERSORTx and (F) clonotypes per million reads assembled using TRUST. Relapse biopsies post-ipi were sampled at time of relapse.