Figure 6. Higher UCD and PTMB Levels Are Associated with Increased Response to Immune Checkpoint Therapy in Mouse Models and Patients.
(A) UCD scores are significantly higher in responders (orange, n = 13) than non-responders (gray, n = 8) to anti-PD1 therapy (Wilcoxon rank-sum test, p < 0.05).
(B) ROC curves showing higher predictive power of PTMB (AUC = 0.77, blue) compared to that obtained via mutational load (AUC = 0.34, red) in predicting the response to anti-PD1 therapy (Roh et al., 2017). In this dataset, UCD scores could not be calculated because the gene expression of UC enzymes was not measured (due to limited coverage of nanostring measurements).
(C) Hydrophobicity (Janin, 1979) of 15 R → Y candidate neopeptides. The triangles denote the changes in the hydrophobicity of the candidate neopeptides in the UC dysregulated versus control cell lines. Among the predicted neopeptides, those that are either predicted to bind to MHC class I (Andreatta and Nielsen, 2016; Jurtz et al., 2017; Karosiene et al., 2012; Zhang et al., 2009; Rasmussen et al., 2016; O’Donnell et al., 2017), or whose AA sequence is found in immune epitope database (IEDB) (Vita et al., 2015), are marked in red (see the STAR Methods). The four R → Y neopeptides predicted to bind to MHC class I show significantly higher hydrophobicity following R → Y mutation (paired one-sided t test p < 0.04).
(D) MC-38 mouse colon cancer cells without UCD (left) and with UCD (right) were injected into C57Bl6 mice. The mice were treated intraperitoneally with anti-PD1 immunotherapy on days 7, 12, 16, and 19. Tumor volume was palpated twice a week. Cancer cells with UCD (induced via the knockdown of ASS1 with shASS1; blue) showed a significantly higher response to anti-PD1 treatment compared to the controls (yellow), as reflected by a significant decrease in tumor volume (n = 20 mice, 5 mice in each group, Wilcoxon rank-sum test, p < 0.007).
(E) Following sacrifice on day 21, flow cytometry analysis shows a significantly increased number of CD8 cytotoxic T cells infiltrating into the excised tumors (n = 20 mice, 5 mice in each group, Wilcoxon rank-sum test, p = 0.01 and 0.3, respectively for shASS1 and EV).
(F) UCD mice treated with anti-PD1 (blue) show significantly attenuated tumor growth compared to the untreated mice (yellow) (p < 0.01, ANOVA with Dunnett’s correction).