克隆巩固和转录重编程界定对免疫检查点抑制剂耐药的非小细胞肺癌

Analysis of pre-treatment non-small cell lung cancers (NSCLCs) has helped identify predictors of response to immune checkpoint inhibitors (ICI), including low PD-L1 expression, targetable drivers alterations ( EGFR , ALK ), and STK11 / KEAP1 mutations. To-date, however, few samples at treatment resistance have been studied, and consequently less is known about the mechanisms contributing to ICI resistance.Methods: Building on our previous analysis Stand Up 2 Cancer-Mark Foundation (SU2C-MARK) Cohort, we identified patients with on or post-treatment samples and performed whole exome (WES) and/or RNA-sequencing, based on tissue availability and quality. Genomic and transcriptomic features in post vs pre-treatment samples were compared. Subclonal evolution in paired samples was assessed using PhylogicNDT, and immune phenotypes were inferred using published gene signatures and deconvolution methods (CIBERSORTx).Results: Building on the original n=393 cohort, 41 patients with on and/or post-treatment samples were identified, with n=45 WES and n=35 RNA-seq on-treatment/post-treatment samples passing QC, for a total of n=445 samples included in the updated cohort, SU2C-MARKv2. N=28 patients had paired samples across treatment time, ranging from 2-5 time points. Only 3 samples had acquired mutations in B2M or JAK2 ; more commonly, post-treatment tumors showed persistence of clones containing STK11 , KEAP1 , and/or ARID1A / SMARCA4 alterations. The proportion of subclonal alterations decreased at resistance, suggesting elimination of passenger-rich antigenic subclones (median 7.9% vs1.9%, p<0.001). Acquired copy number loss in antigen presentation genes in 6p21 ( STAT1/HLA/TAP1/TAP2 ) were observed in 5 treatment pairs, and amplification in 9p24.1 (JAK2/PD-L1/PD-L2) in 4 pairs. In the transcriptional space, resistant tumors demonstrated increased expression of gene sets associated with tumor-intrinsic biology, including MYC, oxidative phosphorylation, and EMT, and decrease in DNA repair genes (ATM). Alterations in immune gene sets were most prominent in on- rather than post-treatment specimens, with increase in T, B and myeloid cell signatures in both responding and non-responding tumors, though numbers were low (n=5). Immune clustering into hot, intermediate, and cold phenotypes confirmed an increase in hot tumors in on-treatment specimens, while post-treatment tumors had predominantly ‘intermediate' immune phenotype.Conclusions: Integrated genomic/transcriptomic analysis of the expanded SU2C-MARKv2 cohort suggests that ICI resistance emerges through elimination of immunogenic subclones and selection for resistant subclones that maintain immune-suppressive transcriptomic phenotypes. Further integration of spatial and single-cell data will define the tumor-immune architecture and identify potential treatment targets.