Serial transcriptomic analyses capture the effects of neoadjuvant immune checkpoint inhibition in resectable gastroesophageal cancer

Introduction: Immune checkpoint inhibition (ICI) is gaining momentum as peri-operative therapy for resectable cancers, however early changes in the tumor microenvironment (TME) during and after neoadjuvant ICI have yet to be characterized. Methods: Bulk RNA sequencing (RNAseq) was performed on 71 serial tumors sampled at baseline, post 2 cycles of neoadjuvant ICI (post-ICI), and at the time of resection, in a cohort of 32 patients with resectable gastroesophageal cancer treated with neoadjuvant nivolumab or nivolumab + relatlimab, followed by concurrent ICI and chemoradiation (NCT03044613). We performed gene set enrichment analyses (GSEA) of RNAseq data, stratified by pathological response and clinical outcomes. Complete (pCR) and major pathological response (MPR) were defined as 0% and ≤10% residual tumor at resection. Results: GSEA revealed an upregulation of interferon alpha, interferon gamma, antigen processing and presentation, and pro-inflammatory M1 macrophage gene sets post-ICI compared to baseline (FDR-adjusted p < 0.006). After chemoradiation, resected tumors showed depletion of DNA repair, chromosome maintenance, cell proliferation and cell cycle progression gene sets, reflective of the cytotoxic effect of therapy (FDR-adjusted p < 10e-06). Notably, in the nivolumab + relatlimab arm, induction of adaptive immune response gene sets and TNFa signaling through NF-kB was noted in resected specimens (FDR-adjusted p < 10e-05). Among patients who attained a pCR, there was an upregulation of interferon alpha, interferon gamma, and antigen processing and presentation gene sets post-ICI (FDR adjusted p < 10e-06). Similarly, in those who attained an MPR there was an upregulation of inflammatory response, interferon gamma, and B cell receptor gene sets (FDR adjusted p < 10e-09), while cellular metabolism and oxidative phosphorylation gene sets were down regulated post-ICI (FDR adjusted p < 0.05). Linking transcriptomic profiles with disease recurrence, we found a downregulation of inflammatory related gene sets post-ICI in recurrent cases (FDR adjusted p < 0.0006). Depletion of oxidative phosphorylation, metabolism, and chromatin regulation gene sets was noted in baseline tumors of patients that attained long overall survival (FDR adjusted p < 10e-05). In post-ICI tumors, there was an upregulation of inflammatory and adaptive response gene sets in patients with longer overall survival (FDR adjusted p < 10e-08), while the oxidative phosphorylation and metabolism gene sets remained suppressed (FDR adjusted p < 0.003). Conclusions: Neoadjuvant ICI induces differential inflammatory and metabolism expression programs that are reflective of pathological responses, recurrence and survival, broadening our understanding of actionable mechanisms of ICI efficacy.