Background: In the Phase III randomized trial (SWOG Lung-MAP S1400I non match trial), adding ipilimumab (I) to nivolumab (N) did not improve survival of patients with advanced, pretreated, immune checkpoint inhibitor naive lung squamous cell carcinoma (SCC). The I+N combination demonstrated superiority in patients with a tumor mutation burden (TMB) ≥10 mt/MB and PD-L1 expression <1% suggesting that a subset of patients may benefit from the addition of I. We leveraged specimens from S1400I to explore the immune signatures associated with outcome across both arms (I+N versus N) and investigate the potential superior benefit from I+N in SCC.

Methods: RNA extracted from baseline FFPE samples from 66/252 patients enrolled in the S1400I trial was received from the SWOG bank with 28 samples considered inadequate due to low input RNA. 38 samples were run on the ncounter platform using the PanCancer Immune Profiling panel using the manufacturer’s instructions with the addition of Human Reference RNA control. Data were processed and normalized using nSolver. All samples passed the post run QC with no batch effect. Using a log-rank test on dichotomized normalized data, we performed time to event analysis to identify genes that correlated with overall survival (OS) and PFS (Progression Free Survival) for all 38 samples and for each arm (23 N and 15 I+N). We ran a Cox model using significant genes identified independently and in association with TMB≥10 and PD-L1 ≥5 thresholds identified in the clinical studies. TIMER and nSolver advanced analysis were used to infer immune cells that correlated to clinical outcomes.

Results: We observed that BLNK, CD163, FCGR2A associated with increased OS (p<0.01), IRF1 and BLNK associated with increased PFS (p<0.01). FADD and MAPK11 associated with poor OS (p<0.01). Cox model analysis confirmed that FADD and MAPK11 were associated with negative clinical outcomes (p<0.05) while CD163 was associated with positive clinical outcome. Incorporating TMB and PD-L1 into the Cox model validated that MAP kinase activity resulted in a negative clinical outcome while CD163 correlated with positive clinical outcomes (p<0.05). Focusing on immune signatures within the I+N arm, we observed higher CD45+ immune cell scores including exhausted CD8+ T cells and neutrophils in responders versus non-responders (p<0.05).

Conclusion: Despite a small dataset, this analysis shows a potential advantage in PFS and OS with increased presence of immune cells including exhausted CD8+ T cells and genes associated with myeloid cells. Validation of these findings is warranted and may refine patient populations that would benefit from this combination strategy.

Acknowledgments: Scientific and financial support: U10CA180888, U10CA180819, U24CA224285, U24CA224316, PACT, PPP and FNIH

Citation Format: Dzifa Y. Duose, Jiexin Zhang, Mary Redman, Baili Zhang, Ethan Cerami, James Lindsay, Joyce Yu, Roshni Biswas, Stephen Van Nostrand, Radim Moravec, Rajyalakshmi Luthra, Gheath Al-Atrash, Karen Kelly, Roy Herbst, Ignacio Wistuba, Scott Gettinger, Lyudmila Bazhenova, J. Jack Lee, Jianjun Zhang, Cara Haymaker. Immune gene expression signatures associated clinical benefit from nivolumab and ipilimumab for previously treated patients with stage IV squamous cell lung cancer: An immune biomarker analysis of phase III SWOG LungMAP S1400I trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1974.