Clinicopathologic, genomic, and tumor microenvironment correlates of aneuploidy and immunotherapy outcomes in NSCLC.
Authors: Alessi Joao Victor Machado , Ricciuti Biagio , Li Yvonne Y. , Gupta Hersh , Lamberti Giuseppe , Recondo Gonzalo , Venkatraman Deepti , Nishino Mizuki , Cherniack Andrew D. , Lindsay James , Sharma Bijaya , Pfaff Kathleen L. , Felt Kristen , Sholl Lynette M. , Rodig Scott J. , Awad Mark M. 
Published: June 2021

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Background: Cancer aneuploidy, an unbalanced number of chromosomes, is associated with somatic mutation rate, expression of proliferative genes, and altered immune signaling. Whether aneuploidy correlates to a distinct immunophenotype or impacts clinical outcomes to immune checkpoint inhibitors (ICIs) in NSCLC is unclear. Methods: In NSCLCs which underwent targeted next-generation sequencing, we retrospectively analyzed the aneuploidy score (AS), defined as the sum of the number of altered chromosome arms. An unbiased recursive partitioning (URP) algorithm was used to investigate an AS cutoff to discriminate responders from non-responders to ICIs. Multiplexed immunofluorescence to quantify CD8+, Foxp3+, PD-1+, and PD-L1 expression was performed to determine differences in tumor immune cells subsets according to AS cutoff. Results: Among 436 NSCLCs identified, stage I tumors (median AS 1) had significantly lower median AS (mAS) than stage IV cancers (mAS 7, P < 0.001), stage III (mAS 4, P = 0.03), and numerically lower compared to stage II cancers (mAS 3, P = 0.18). We found no difference in the mAS across tumors with a PD-L1 tumor proportion score of ≥50%, 1-49%, or < 1% (mAS 5 vs 7 vs 6, respectively, P = 0.26), nor was there any correlation between aneuploidy and TMB when taken as continuous variables (Spearman R: 0.074, P = 0.12). A total of 279 advanced NSCLCs with available aneuploidy scores were treated with ICIs. An URP analysis identified an AS of 2 as the strongest discriminator of objective response to ICI. Compared to pts with an AS > 2 (N = 207, 74.2%), pts with AS ≤2 (N = 72, 25.8%) had a significantly higher objective response rate (ORR 43.0% vs 19.8%, P < 0.001), a significantly longer median progression-free survival (mPFS 6.2 vs 2.9 months, HR: 0.70 [95% CI: 0.52-0.94], P = 0.02), and a significantly longer median overall survival (mOS 19.8 vs 13.8 months, HR: 0.66 [95% CI: 0.47-0.94], P = 0.02) to treatment with ICIs. After adjusting for other variables such as performance status, presence of oncogenic driver mutation, PD-L1, TMB, and line of treatment, AS was significantly associated with improved mPFS (HR: 0.72 [95% CI: 0.52-0.99], P = 0.04) and mOS (HR: 0.64 [95% CI: 0.44-0.94], P = 0.02). By contrast, among pts who received first-line platinum doublet chemotherapy without ICI, an AS ≤2 (N = 29), when compared to an AS > 2 (N = 56), did not correlate with improved ORR (55.2% vs 44.6%, P = 0.4) or PFS (5.3 vs 4.8 months, HR 0.83 [95% CI: 0.5-1.3], P = 0.43). Among 179 NSCLCs profiled by multiplex immunofluorescence, compared to cancers with an AS > 2, those with low aneuploidy had significantly higher numbers of CD8+, Foxp3+, PD-1+ immune cells, and PD-1+ CD8+ T cell, both intratumorally and when looking at the total numbers of cells within the tumor and at the tumor-stroma interface. Conclusions: NSCLCs with low aneuploidy have a distinct immune microenvironment and more favorable outcomes to ICIs.