Abstract 5903: Clinical immune and genomic profiling of STK11 mutant non-squamous non-small cell lung cancer
Authors: Yau Edwin , Pabla Sarabjot , Glenn Sean , Papanicolau-Sengos Antonios , Nesline Mary , Dy Grace , Morrison Carl 
Published: September 2020

Abstract
Background: The use of immune PD-1/PD-L1 checkpoint inhibitors (ICI) has dramatically altered the treatment of advanced Non-Small Cell Lung Cancer (NSCLC). However, a large proportion of patients with NSCLC do not derive clinical benefit from ICI treatment. Recent studies have identified STK11 mutations leading to loss of LKB1 in NSCLC as drivers of primary resistance to ICI treatment. Using a clinical cohort of patients whose tumors underwent comprehensive genomic and immune transcriptomic analysis, we characterized the immune gene expression profile of STK11 mutant non-squamous NSCLC tumors and identified TRIM29 as a potential therapeutic target in STK11 mutant non-squamous NSCLC.
Methods: We performed comprehensive analysis of the genomic and immunological landscape of 199 formalin-fixed, paraffin-embedded tumor samples (obtained prior to ICI treatment) from advanced stage non-squamous NSCLC patients treated at Roswell Park Comprehensive Cancer Center using a CLIA-certified laboratory test that included targeted NGS genomic sequencing, gene fusion analysis, and RNA-seq of 394 immune transcripts. Differential gene expression analysis was performed using R/Bioconductor package limma with Benjamini-Hochberg adjusted p-values reported. This study was approved by Roswell Park internal review board review (protocol BDR 091817) according to institutional policy for nonhuman subjects research.
Results: Among the cohort of 199 cases, 32 contained truncating STK11 mutations. STK11 mutant cases showed an immunosuppressive environment with decreased PD-L1 expression (p=0.01) and decreased T-cell inflammation gene expression signature (p=0.0029) consistent with prior published cohorts. Analysis of differentially expressed immune genes signatures showed significant decreases in antigen presentation (p=0.015) and processing (p=0.044), NK cell activation (p=0.039), chemokine and cytokine signaling (p=0.044), immune checkpoint pathways (p=0.015), innate immune response (p=0.04), and interferon signaling (p=0.039). The top upregulated gene in STK11 mutant cases was TRIM29 (p=0.03). Other overexpressed targets included ID3 (p=0.009), KRT7 (p=0.02), and NOTCH3 (p=0.05). Interrogation of TCGA LUAD dataset also demonstrated elevated TRIM29 expression (p=0.006) in STK11-mutant compared to STK11-wild-type samples and we also confirmed elevated TRIM29 RNA and protein expression in a panel of STK11 mutant NSCLC human cell lines. Immunohistochemical staining of a cohort of 68 KRAS mutant NSLCLC patient samples also showed higher levels of TRIM29 protein staining in STK11 mutant samples. Knockdown of TRIM29 using shRNA inhibited growth of STK11 mutant tumor xenografts. TRIM29 is a E3 ubiquitin ligase and we evaluated known targets of TRIM29 and found decreased TAB2 expression in STK11 mutant NSCLC. Notably, TAB2 is also regulated by SIK1/3, which have been recently identified as signaling partners with STK11. TRIM29 has been implicated as a mediator of processes also involved in STK11 tumorigenesis such as cellular metabolism, DNA damage repair, innate immunity, and squamous differentiation.
Conclusion: Using a large clinical cohort of non-squamous NSCLC patients we characterized the immunosuppressive environment of STK11 mutant tumors and identified the E3 ubiquitin ligase TRIM29 as a potential therapeutic target.
Citation Format: Edwin Yau, Sarabjot Pabla, Sean Glenn, Antonios Papanicolau-Sengos, Mary Nesline, Grace Dy, Carl Morrison. Clinical immune and genomic profiling of STK11 mutant non-squamous non-small cell lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5903.