Somatic 9p24.1 alterations in HPV^- head and neck squamous cancer dictate immune microenvironment and anti-PD-1 checkpoint inhibitor activity.

Finally, we note that there is a highly significant co-occurrence of 9p21.3 deletion (arm or focal) and 9p24.1 deletion (arm or focal) ( P =1.82E-57), and focal deletion of 9p21.3 and 9p24.1 ( P =2.03E-07), suggesting that the effects seen for 9p21.3 loss (e.g., on PD-L1 expression) are likely due to simultaneous co-deletion of 9p24.1. 9p24.1 SCNA Associations With TME Phenotype in Independent HPV – HNSC Validation Cohort.

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Although limited by the small sample size ( n = 20), analysis of the 9p24.1, but not 9p21.3, loss subgroup showed a trend for the prediction of low immune score (9p24.1: β = –0.96, q = 0.10; 9p21.3: β = –0.39, q = 0.41) and CD8 T-cell level (9p24.1: β = –1.00, q = 0.11; 9p21.3: β = –0.35, q = 0.46).

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