Abstract A083: Integrated multi-omic analysis and CRISPR screening identify GPX2 as a critical vulnerability in high-risk lung adenocarcinoma
TL;DR
An integrated multi-omic approach presented here identified GPX2 as a critical vulnerability in a well-defined LUAD subpopulation and provides a rationale for targeting the NFE2L2/GPX2 axis, offering a strategic opportunity for therapeutic intervention.
Abstract
Targeted therapies have transformed the management of lung adenocarcinoma (LUAD), yet further clinical progress is hindered by its molecular complexity. Previous efforts to characterize this heterogeneity have been constrained by small cohorts, limiting the discovery of therapeutic targets. We leveraged a large-scale real-world dataset (RWD) to define a LUAD subpopulation with high unmet clinical need. We integrated gene network modeling and spatial transcriptomics to identify key molecular drivers and functionally validated candidate gene targets using CRISPR screening in subtype-matched patient-derived organoids (PDOs). De-identified clinico-genomic records from LUAD patients profiled with Tempus xT (DNA) and xR (RNA)-seq assays were analyzed (n=7956). Non-negative matrix factorization applied to gene expression data was used to identify molecular subtypes. Progression free survival (PFS), defined as the time from the start of first metastatic therapy to the date of first progression or death from any cause, was assessed in a subset of patients with available data (17.6% of total samples). A classifier trained on tumor-intrinsic features was used to assign subtypes to 36 LUAD PDOs and 19 LUAD tissue samples profiled with the Visium HD spatial transcriptomics platform. A gene regulatory network was modeled using the Priori algorithm by weighting known TF-target associations from the DoRothEA database with xR data. CRISPR/Cas9 screening was performed in PDOs, followed by CellTiter-Glo viability and xR assays to evaluate the functional and transcriptomic impact of gene knockouts. Six distinct molecular subtypes of LUAD were identified (C1-C6). The C5 subtype (23.15% of total samples) exhibited the worst prognosis (PFS 5.6 months, 95% CI 4.3-7.4) with high prevalence of STK11 (36.85%), KEAP1 (19.67%), and SMARCA4 (15.95%) mutations. Spatial transcriptomics analysis revealed that the C5 subtype was significantly enriched for three distinct niches (localized cellular micro-environments): tertiary lymphoid structure, macrophage-dominated myeloid, and mucinous malignant. Gene co-expression modules associated with the C5 subtype were enriched for NFE2L2 (NRF2) transcription factor pathways. The NFE2L2 gene regulatory network was most transcriptionally active in the C5 subtype. Spatially, NFE2L2 network activity was highest in the mucinous malignant niche and was driven primarily by club cells and malignant cells. Knockdown (KD) of key network nodes (NFE2L2, GPX2, NQO1) in C5 subtype-matched PDOs led to a reversal of the NFE2L2 signature. Additionally, GPX2 KD led to significantly higher viability loss in C5 versus C1 subtype-matched PDOs (p < 0.001). The integrated multi-omic approach presented here identified GPX2 as a critical vulnerability in a well-defined LUAD subpopulation. These findings provide a rationale for targeting the NFE2L2/GPX2 axis, offering a strategic opportunity for therapeutic intervention. Akul Singhania, Kayla R. Bastian, Yajas Shah, Swati Kaushik, Brandon L. Mapes, Lee F. Langer, Yaakov E. Stern, Prerna Jain, Ezgi Karaesmen Rizvi, Samantha Cowher, Chi-Sing Ho, Brian Roberts, Nick Callamaras, Richard A. Klinghoffer, Justin Guinney, Radia M. Johnson. Integrated multi-omic analysis and CRISPR screening identify GPX2 as a critical vulnerability in high-risk lung adenocarcinoma [abstract]. In: Proceedings of AACR Drug Discovery and Development (AACR D3) Conference; 2026 Jul 21-24; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(14_Suppl):Abstract nr A083.