Abstract 7166: Spatially resolved protein profiling of tumor and immune microenvironment in EGFR mutant NSCLC with transformation to SCLC

Abstract Background: Approximately 3-10% of EGFR-mutant non-small cell lung cancer (NSCLC) cases transform into small cell lung cancer (SCLC) as a resistance mechanism to third-generation EGFR tyrosine kinase inhibitors (TKIs). The mechanisms driving this transformation are poorly understood. This study investigates proteomic differences between pre-transformed EGFR adenocarcinoma (preADC) and post-transformed SCLC (postSCLC) to identify underlying mechanisms and therapeutic vulnerabilities. Methods: Nanostring GeoMx® Digital Spatial Profiling (DSP) technology was used to analyze seventy protein biomarkers in FFPE patient samples. Two patient cohorts were analyzed: Cohort one included seven patients, with one patient having a preADC sample and six patients having postSCLC samples. Cohort two included three patients, each providing paired preADC and postSCLC samples (3 preADC and 4 postSCLC samples in total). Up to 12 regions of interest (ROIs) were selected by expert pathologists from tumor areas, segmented into Tumor and TME compartments based on the expression of morphology markers (pan-CK, synaptophysin, and CD45). Results: After integrating both cohorts and correcting for batch effects, UMAP and heatmap visualizations showed clear separation between preADC and postSCLC tumor segments. Differential protein expression analysis revealed that preADC tumors exhibited increased expression of immune regulatory proteins, including IDO1, VISTA, INPP4B, MET, Tim-3, CD45 and STING, indicating active immune evasion. In contrast, postSCLC tumors showed elevated expression of CD56, PARP, BIM, Ki-67 and pan-AKT, which aligns with the high CD56 expression characteristic of SCLC, dysregulated DNA damage repair pathways, and AKT pathway activation implicated in NSCLC to SCLC transformation. Further comparison of protein expression in the TME segments revealed more abundant expression of CD45, CD11c, and CD4 in preADC TME, while postSCLC TME exhibited higher levels of GZMB, CD56, and PARP. FDR < 0.05 was used as the cut-off. These TME findings indicate an "immune-cold" phenotype in SCLC, characterized by scarce immune cell infiltration and increased resistance to apoptosis. In addition, protein expression panels identified promising immune checkpoint as potential therapeutic targets including B7H3 and LAG3 in both preADC and postSCLC samples. Conclusions: These results highlight molecular and immune changes during the preADC to postSCLC transformation. The shift in tumor and TME protein expressions in postSCLC reflects an increasingly aggressive tumor phenotype, with changes in immune suppression, DNA damage and apoptosis pathways. These findings suggest potential therapeutic targets for EGFR-mutant NSCLC with SCLC transformation. Citation Format: Hong Chen, Bingnan Zhang, Alejandra Serrano, Sharia Hernandez, Wei Lu, Santiago Trevino, Natalie Vokes, Ximeng Liu, Yanhua Tian, Bo Zhu, Monique B. Nilsson, John V. Heymach, Jianjun Zhang, Luisa Solis Soto, Carl M. Gay, Lauren A. Byers, Xiuning Le. Spatially resolved protein profiling of tumor and immune microenvironment in EGFR mutant NSCLC with transformation to SCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7166.