Fig. 6: cGEPs associated with ICI response.

a, UMAPs of the melanoma dataset showing TCAT predicted lineage; the CD4-naive and exhaustion cGEPs; the ASA and cell cycle scores; TCF7 expression; and treatment status and response. b, Associations of cGEP usage with ICI response in CD4⁺ T cells of pretreatment melanoma. Dots are colored by cGEP type. x axis shows the average difference in usage between nonresponders and responders. y axis shows the −log₁₀ two-tailed P value. c–e, Average ASA score, cell cycle score and CD4-naive cGEP usage in CD4⁺ T cells from pretreatment melanomas and NMSC tumors and combined pretreatment and post-treatment CRC. The average scores are mean and variance normalized. P values are one-tailed t-tests for melanoma and NMSC and mixed linear regression P values for CRC. P value in the title is a meta-analysis of the P values across the three cancer types. *P < 0.05. Boxes represent the interquartile range and whiskers represent 1.5 times interquartile range. The box center line indicates the median. Sample sizes shown are n = 9, n = 6 and n = 15 for responders in melanoma, NMSC and CRC, respectively, and n = 10, n = 7 and n = 4 in nonresponders in melanoma, NMSC and CRC. f, Same as b in pretreatment NMSC. g, Same as b in combined pretreatment and post-treatment CRC, but showing coefficients and P values from mixed linear regression analysis, controlling for treatment time point and donor of origin.