Neoadjuvant chemoimmunotherapy (CI) for NSCLC is a promising strategy that yields high rates of complete pathological responses (CPR) that are associated with long-term survival. We analyzed the tumor microenvironment by using gene expression profiling in patients from NADIM trial to identify biomarkers predicting CPR.
RNAs extracted from whole sections of pre-treatment tumors of 14 patients enrolled in NADIM trial (NCT03081689) were sequenced using the Oncomine® Immune Response Research Assay panel. Differential-expressed genes between groups and pathway enrichment analysis were assessed using DESeq2 and Gene Set Enrichment Analysis (GSEA). CIBERSORTx was used to estimate the proportions of immune cells subtypes. Results were correlated with pathological response groups: complete (CPR, n=9) and non-complete (non-CPR, n=5) responders.
Up to 25 genes were identified as differentially expressed between CPR and non-CPR patients. Among them, 17 were upregulated in CPR compared to non-CPR: involved in type II interferon signalling (FASLG, CXCL13, CXCL10, CXCL9 and IFNG), NK cell markers (NCR1, KIR2DL3, GNLY) or lymphocyte enrichment (NKG7, GZMB) depicting a pro-inflammatory phenotype in pre-treatment tumour samples of CPR patients. Similarly, GSEA analysis revealed in CPR patients an up-regulation of pathways related to TCR co-expression, lymphocyte infiltrate, type II interferon signalling and antigen processing, as well as a downregulation of pathways related to tumour markers, proliferation or PD-1 signalling. Finally, CPR patients had a higher proportion of follicular helper T cells, activated NK cells, M1 macrophages, resting dendritic cells and absolute score of immune cells than non-CPR patients, being the proportion of M1 macrophages significantly different (p=0.002). The AUC ROC for response prediction based on IFNG, GZMB expression or M1 macrophages proportion was 1.000 (p=0.0027), 0.911 (p=0.0136) and 0.9778 (p=0.004), respectively.
In our study, a pro-inflammatory profile measured in the pre-treatment tissue by RNA-sequencing is associated with CPR following neoadjuvant CI in patients with stage IIIA NSCLC.
Clinical trial identification
Legal entity responsible for the study
Bristol Myers Squibb, Thermofisher provided reagents for RNA-seq. Spanish Lung Cancer Group promoted the NADIM study. ‘‘Instituto de Salud Carlos III’’ (ISCIII), European Regional Development Fund (ERDF), Ministry of Science and Innovation, European Social Fund (ESF) and Comunidad de Madrid supported authors’ contracts.
M. Provencio Pulla: Non-Financial Interests, Institutional, Research Grant: Bristol Myers Squibb; Non-Financial Interests, Institutional, Research Grant: Roche; Non-Financial Interests, Institutional, Research Grant: AstraZeneca; Non-Financial Interests, Personal, Advisory Board: Bristol Myers Squibb; Non-Financial Interests, Personal, Advisory Board: Roche; Non-Financial Interests, Personal, Advisory Board: AstraZeneca; Non-Financial Interests, Personal, Advisory Board: MSD; Non-Financial Interests, Personal, Advisory Board: Takeda. All other authors have declared no conflicts of interest.