Non-Small Cell Lung Cancer Patients Treated with Anti-PD1 Immunotherapy Show Distinct Microbial Signatures and Metabolic Pathways According to Clinical Outcomes

Abstract

Background: Clinical outcomes of immune checkpoint inhibitor (ICI)-treated non-small cell lung cancer (NSCLC) patients might be associated with the gut metagenome. Methods: Sixty-two Caucasian advanced-stage NSCLC patients treated with anti-PD1 immunotherapy were included. Gut bacterial signatures were evaluated by metagenomic sequencing and correlated with progression-free survival (PFS), PD-L1 expression defined by immunohistochemistry, and other clinicopathological parameters. The predictive role of PFS-related key bacteria was confirmed with multivariate statistical models and validated on an additional patient cohort (n=60). The functional microbial signature of distinct patient groups were determined by analyzing metabolic pathways. A random forest (RF) machine learning algorithm was used to assess the predictive power of taxonomic and metabolic microbial signatures. Results: Alpha-diversity showed no significant difference in any comparison. However, there was a significant difference in beta-diversity between patients with long- (>6 months) vs. short (≤6 months) PFS and between chemotherapy (CHT)-treated vs. CHT-naive cases. Short PFS was associated with increased abundance of Firmicutes (F) and Actinobacteria phyla, whereas elevated abundance of Euryarcheota was specific for low-PD-L1 expression. F/Bacteroides (F/B) ratio was significantly increased in patients with short PFS. Multivariate analysis revealed an association between Alistipes shahii, Alistipes finegoldii, Barnesiella visceriola, and long PFS. In contrast, Streptococcus salivarius, Streptococcus vestibularis, and Bifidobacterium breve were associated with short PFS. Taxonomic profiles performed superiorly in predicting PFS (AUC=0.74), while metabolic pathways including Amino Acid Synthesis and Fermentation were better predictors of PD-L1 expression (AUC=0.87). Conclusion: The specific metagenomic features of the gut microbiome including bacterial taxonomy and metabolic pathways are suggestive of ICI efficacy and PD-L1 expression in NSCLC patients.

The Gut Microbiome from a Biomarker to a Novel Therapeutic Strategy for Immunotherapy Response in Patients with Lung Cancer

“…Patients with PFS > 6 months, on the other hand, were associated with a higher abundance of Alistipes spp. and Barnesiella visceriola [37]. Furthermore, another study on metastatic colorectal cancer patients and NSCLC patients treated by cetuximab + avelumab showed that fecal samples of long-term responders had particularly higher populations of two butyrate-producing bacteria, Agathobacter M104/1 and Blautia SR1/5 [38].…”

Immunologic constant of rejection as a predictive biomarker of immune checkpoint inhibitors efficacy in non-small cell lung cancer.

“…The independent predictive value of this signature was validated in a prospective series of 37 NSCLC treated with nivolumab, independently from PDL1 expression by IHC [15], and more recently in patients treated with pembrolizumab, in a pan-cancer clinical trial performed across 20 tumor types, including lung cancer [16]. Finally, methylation profiles and microbiota assessment turned out to be hardly operable in daily care [17][18][19].…”

Gut microbiota and dietary intervention: affecting immunotherapy efficacy in non–small cell lung cancer

“…In one study, Granulicatella showed a significant association with responders to anti-PD-1 therapy and thus could be used as a biomarker for prognosis and diagnosis (56). Other studies have shown that the presence of Alistipes is related to better results in ICIs treatment (57), and Alistipes putredinis is reduced in patients with advanced NSCLC who respond to anti-PD-1 immunotherapy (34). Moreover, the overexpression of Alistipes indistinctus in NSCLC responders was found to be effective in restoring the efficacy of ICIs therapy (27).…”

“…Bifidobacteria are key intestinal beneficial microorganisms, which as a type of physiologically beneficial bacteria, can exert an antitumor effect. Bifidobacterium species have been shown to be strongly associated with ICIs efficacy (57,61), mainly by promoting the activation of dendritic cells (DCs) under homeostasis, which in turn improves the effector function of tumor-specific CD8+ T cells (29). Sivan (29) et al showed that the therapeutic effect of Bifidobacterium was abolished in mice lacking CD8+ T cells, suggesting that the mechanism was not direct but exerted through the host antitumor T-cell response.…”