Abstract 6629: Genomic and immunophenotypic landscape of acquired resistance to PD-(L)1 blockade in non-small cell lung cancer
Authors: Ricciuti Biagio , Lamberti Giuseppe , Puchala Sreekar , Mahadevan Navin , Alessi Joao , Wang Xinan , Li Yvonne , Pecci Federica , Federico Alessandro Di , Gandhi Malini , Barrichello Adriana , Vaz Victor , Pangilinan Andy , Haradon Danielle , Lee Elinton , Gupta Hersh , Nishino Mizuki , Cherniack Andrew , Rodig Scott , Sholl Lynette , Umeton Renato , Awad MArk M. 
Published: June 2023

Abstract
Background: Despite immune checkpoint inhibition (ICI) has extended survival in patients (pts) with non-small cell lung cancer (NSCLC), acquired resistance to ICI develops after an initial clinical benefit. However, the mechanisms underlying the development of acquired resistance to ICI in NSCLC are largely unknown.
Methods: Tumor genomic profiling, immune cell subsets assessment from standard haematoxylin/eosin (H&E) stained slides using machine learning, multiplexed immunofluorescence (CD8, PD1, PD-L1, Foxp3, CK7), and HLA-I immunohistochemistry (IHC) were performed on matched pre and post ICI tumor biopsies from pts with NSCLC treated with ICI at the Dana-Farber Cancer Institute who developed acquired resistance to ICI.
Results: Among 1823 pts with advanced NSCLC who received ICI, 80 developed acquired resistance to treatment and had matched pre- and post-ICI tissue samples for correlative analysis. Putative resistance mutations were identified in 27.3% of cases. The most common acquired loss-of-function mutations included STK11 (9.1%), B2M (6.5%), NF1/2 (5.2%), SMARCA4 (5.2%), APC (3.9%), KEAP1 (2.6%), and JAK1 (2.6%). In addition, acquired activating mutations were found in PI3KCA (3.9%) and SOS1 (1.3%). In examining copy number variations (CNVs), we identified acquired CNVs in 49.3% (38/77) of ICI-resistant samples, including heterozygous loss of B2M (23.4%), STK11 (16.8%), SMARCA4 (16.9%), KEAP1 (15.6%), PTEN (10.4%), CDKN2A/B (9.1%) and PD-L1/PD-L2 genes (9.1%), among others. Importantly, we also noted acquired homozygous deletions in CDKN2A/B (9.1%), PD-L1/PD-L2 (1.3%) and JAK2 (1.3%), and amplification in MDM2 (5.2%), KRAS (3.9%) and MYC (2.6%), at the time of resistance to ICI. Among 16 cases with pre- and post-ICI H&E stained slides, digital pathology analysis showed a significant decrease in the density of intratumoral lymphocytes in ICI-resistant tumor samples compared to pre-ICI samples (88 vs 36 cells/mm2, P=0.03). Consistently, among 6 pts with pre- and post-ICI multiplexed immunofluorescence we observed a significant decrease in CD8+ PD1+ T cells in ICI-resistant vs pre-ICI tumor samples (24 vs 10 cells/mm2, P=0.01). Among pts with tissue available for HLA-I IHC (N=9), we found a significant decrease in HLA-I expression by H-score at the time of acquired resistance (300 vs 260, P=0.03). In control cohorts of pts with pre- and post-chemotherapy (CT) (N=32) or targeted therapies (TT) (N=89) tumor genomic profiling no acquired mutations in STK11, KEAP1, B2M, JAK1, APC, SOS1 were detected. Similarly, intervening chemotherapy and targeted therapies were not associated with changes in lymphocytes density and HLA-I expression.
Conclusion: Mechanisms of acquired resistance to ICI are heterogenous, including both genomic and immunophenotypic factors. New therapeutic strategies are required to delay and overcome ICI resistance in pts with NSCLC.
Citation Format: Biagio Ricciuti, Giuseppe Lamberti, Sreekar Puchala, Navin Mahadevan, Joao Alessi, Xinan Wang, Yvonne Li, Federica Pecci, Alessandro Di Federico, Malini Gandhi, Adriana Barrichello, Victor Vaz, Andy Pangilinan, Danielle Haradon, Elinton Lee, Hersh Gupta, Mizuki Nishino, Andrew Cherniack, Scott Rodig, Lynette Sholl, Renato Umeton, MArk M. Awad. Genomic and immunophenotypic landscape of acquired resistance to PD-(L)1 blockade in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6629.