FIG 5.

Clonal evolution is associated with response to ICI. All four patients were treated with nivolumab plus cabozantinib, and clonal evolutionary analysis was performed using PhylogicNDT. (A) Pt14 (FFPE samples) was marked by an almost complete loss of the clonal population and was disease-free at 26 months post-therapy. (B) Pt15 (ctDNA samples) showed modest decreases in some subclones and progressed after 13 months. (C) Pt19 (ctDNA) and (D) Pt18 (FFPE) had virtually no change in clonal cancer cell fractions and were associated with early relapses (6 and 2 months post-treatment, respectively). (E) TMB was highest in Pt14, who was progression-free post-treatment, and progressively decreased with time to progression in patients 15, 19, and 18. (F) CYT had a similar trend within these patients (RNAseq was unavailable for patient 19). (G) Pt14 has increased antitumor and decreased protumor (M0 and M2 macrophages) immune compartment proportions compared with other samples (CIBERSORTx). Immune cell labels: antitumor (blue)and protumor (red). CCF, cancer cell fraction; ctDNA, circulating tumor DNA; CYT, cytolytic activity; FFPE, formalin-fixed, paraffin-embedded; ICI, immune checkpoint inhibitor; NK, natural killer; Pt, patient; TMB, tumor mutational burden; TTP, time to progression; WES, whole-exome sequencing.