Impact of aneuploidy and chromosome 9p loss on tumor immune microenvironment and immune checkpoint inhibitor efficacy in non-small cell lung cancer.

BACKGROUND: Although gene-level copy-number alterations have been studied as a potential biomarker of immunotherapy efficacy in non-small cell lung cancer (NSCLC), the impact of aneuploidy burden and chromosomal arm-level events on immune checkpoint inhibitor (ICI) efficacy in NSCLC is uncertain.METHODS: Patients who received PD-(L)1 inhibitor at two academic centers were included. Across all 22 chromosomes analyzed, an arm was considered altered if at least 70% of its territory was either gained or deleted. Among nonsquamous NSCLCs which underwent targeted next-generation sequencing, we retrospectively quantified aneuploidy using the adjusted fraction of chromosomal arm alterations (FAA), defined as the number of altered chromosome arms divided by the number of chromosome arms assessed, adjusted for tumor purity.RESULTS: Among 2293 nonsquamous NSCLCs identified, the median FAA (mFAA) increased with more advanced cancer stage and decreased with higher PD-L1 tumor proportion score (TPS) levels (mFAA in TPS <1%: 0.09, TPS 1-49%: 0.08, TPS ≥50%: 0.05, P<0.0001). There was a very weak correlation between FAA and tumor mutational burden when taken as continuous variables (R: 0.07, P=0.0005). A total of 765 advanced nonsquamous NSCLCs with available FAA values were treated with ICIs. With decreasing FAA tertiles, there was a progressive improvement in objective response rate (ORR 15.1% in upper tertile vs 23.2% in middle tertile vs 28.4% in lowest tertile, P=0.001), median progression-free survival (mPFS 2.5 vs 3.3 vs 4.1 months, P<0.0001), and median overall survival (mOS 12.5 vs 13.9 vs 16.4 months, P=0.006), respectively. In the arm-level enrichment analysis, chromosome 9p loss (OR: 0.22, Q=0.0002) and chromosome 1q gain (OR: 0.43, Q=0.002) were significantly enriched in ICI non-responders after false discovery rate adjustment. Compared to NSCLCs without chromosome 9p loss (N=452), those with 9p loss (N=154), had a lower ORR (28.1% vs 7.8%, P<0.0001), a shorter mPFS (4.1 vs 2.3 months, P<0.0001), and a shorter mOS (18.0 vs 9.6 months, P<0.0001) to immunotherapy. Additionally, among NSCLCs with high PD-L1 expression (TPS ≥50%), chromosome 9p loss was associated with lower ORR (43% vs 6%, P<0.0001), shorter mPFS (6.4 vs 2.6 months, P=0.0006), and shorter mOS (30.2 vs 14.3 months, P=0.0008) to immunotherapy compared to NSCLCs without 9p loss. In multivariable analysis, adjusting for key variables including FAA, chromosome 9p loss, but not 1q gain, retained a significant impact on ORR (HR: 0.25, P<0.001), mPFS (HR: 1.49, P=0.001), and mOS (HR: 1.47, P=0.003). Multiplexed immunofluorescence and computational deconvolution of RNA sequencing data demonstrated that tumors with either high FAA levels or chromosome 9p loss had significantly fewer tumor-associated cytotoxic immune cells.CONCLUSION: Nonsquamous NSCLCs with high aneuploidy and chromosome 9p loss have a distinct tumor immune microenvironment and less favorable outcomes to ICIs.