Naqash, Abdul Rafeh, Floudas, Charalampos S., Aber, Etan, Maoz, Asaf, Nassar, Amin H., Adib, Elio, Choucair, Khalil, Xiu, Joanne, Baca, Yasmine, Ricciuti, Biagio, Alessi, Joao V., Awad, Mark M., Kim, Chul, Judd, Julia, Raez, Luis E., Lopes, Gilberto, Nieva, Jorge J., Borghaei, Hossein, Takebe, Naoko, and Ma, Patrick C.
PURPOSE: Non–small-cell lung cancer (NSCLC) with STK11 mut has inferior outcomes to immune checkpoint inhibitors (ICIs). Using multiomics, we evaluated whether a subtype of STK11 mut NSCLC with a uniquely inflamed tumor immune microenvironment (TIME) harboring TP53 comutations could have favorable outcomes to ICIs. PATIENTS AND METHODS: NSCLC tumors (N = 16,896) were analyzed by next-generation sequencing (DNA-Seq/592 genes). A subset (n = 5,034) underwent gene expression profiling (RNA-Seq/whole transcriptome). Exome-level neoantigen load for STK11 mut NSCLC was obtained from published pan-immune analysis. Tumor immune cell content was obtained from transcriptome profiles using the microenvironment cell population (MCP) counter. ICI data from POPLAR/OAK (n = 34) and the study by Rizvi et al (n = 49) were used to model progression-free survival (PFS), and a separate ICI-treated cohort (n = 53) from Dana-Farber Cancer Institute (DFCI) was used to assess time to treatment failure (TTF) and tumor RECIST response for STK11 mut TP53 mut versus STK11 mut TP53 wt NSCLC. RESULTS: Overall, 12.6% of NSCLC tumors had a STK11 mut with the proportions of tumor mutational burden (TMB)-high (≥10 mut/Mb), PD-L1 ≥50%, and microsatellite instability-high being 38.3%, 11.8%, and 0.72%, respectively. Unsupervised hierarchical clustering of STK11 mut (n = 463) for stimulator of interferon-gamma (STING) pathway genes identified a STING-high cluster, which was significantly enriched in TP53 mut NSCLC (P <.01). Compared with STK11 mut TP53 wt, tumors with STK11 mut TP53 mut had higher CD8+T cells and natural killer cells (P <.01), higher TMB (P <.001) and neoantigen load (P <.001), and increased expression of MYC and HIF-1A (P <.01), along with higher expression (P <.01) of glycolysis/glutamine metabolism genes. Meta-analysis of data from OAK/POPLAR and the study by Rizvi et al showed a trend toward improved PFS in patients with STK11 mut TP53 mut. In the DFCI cohort, compared with the STK11 mut TP53 wt cohort, the STK11 mut TP53 mut tumors had higher objective response rates (42.9% v 16.7%; P =.04) and also had longer TTF (14.5 v 4.5 months, P adj =.054) with ICI. CONCLUSION: STK11 mut NSCLC with TP53 comutation is a distinct subgroup with an immunologically active TIME and metabolic reprogramming. These properties should be exploited to guide patient selection for novel ICI-based combination approaches. [ABSTRACT FROM AUTHOR]