Intratumoral Immune Heterogeneity Drives Divergent Outcomes to PD-(L)1 Blockade in Lung Cancer

Abstract Purpose: Clinical outcomes with immune checkpoint inhibitors (ICI) in non–small cell lung cancer (NSCLC) range from durable disease control to rapid progression. Current biomarkers have a limited ability to predict these divergent outcomes. Experimental Design: Spatially resolved immune subtyping in the TRACERx421 multiregion cohort was used to assess intratumoral immune heterogeneity (ITIH), defined as coexisting immune-enriched and immune-depleted regions. A computational model was used to infer ITIH from single samples, classifying tumors as homogenously immune-enriched (Hom-IE), heterogeneously immune-enriched, heterogeneously immune-depleted, and homogenously immune-depleted. ITIH was validated by digital pathology and evaluated in three independent cohorts (n = 1,085) of patients with advanced NSCLC treated with ICIs. Results: In TRACERx421, ITIH was associated with differences in immune programs among tumors otherwise classified within the same immune subtype. Single-sample ITIH inference recapitulated these patterns, as supported by gradients of tumor-infiltrating lymphocytes detected via digital pathology. Across cohorts, Hom-IE tumors demonstrated longer overall survival (OS) compared with other groups (34.6 vs. 12.1–16.6 months in cohort A; 21.9 vs. 8.4–13.3 months in cohort B; and 22.6 vs. 11.3–13.4 months in cohort C). Hom-IE tumors were associated with longer OS regardless of PD-L1 status. Consistently, among PD-L1-low/negative tumors, Hom-IE tumors showed significantly longer OS compared with their non–Hom-IE counterparts. Conversely, the detrimental effects of KEAP1/STK11 mutations persisted in the Hom-IE background. Conclusions: These findings demonstrate that ITIH can be assessed from individual tumor samples, identify a microenvironment state associated with long-term benefit from immunotherapy, and provide an additional layer of resolution to established and emerging biomarkers.