Structural mimicry of the TOP1 cleavage complex by intratumoural bacterial proteins as a possible mechanism for geographical variation in TOP1 inhibitor efficacy in non-small cell lung cancer.

Abstract

e15039 Background: We previously demonstrated that microbiome-derived proteins with sequence homology to human topoisomerase I (TOP1) are differentially enriched between US and Japanese populations and associated with discordant clinical trial outcomes (Lam et al., 2024). While these findings suggested a possible role for bacterial modulation of TOP1 inhibitor (TOP1i) efficacy, the underlying mechanism remained unclear. Here, we present the results of a deep structural analysis to determine whether TOP1-like bacterial proteins mimic the drug-interacting region of the TOP1-DNA cleavage complex, potentially contributing to differences in the efficacy of TOPi-based interventions, such as antibody-drug conjugates (ADCs). Methods: We extended our previous analysis by integrating intratumoural microbiome datasets from geographically diverse adult populations. Candidate bacterial proteins were prioritised based on sample prevalence and sequence identity with human TOP1. Crystallographic TOP1-DNA-drug ternary complexes of TOP1i analogues, including camptothecin and topotecan, were used to define the binding region at the protein-DNA interface surrounding the cleavage site. Structural alignment and protein folding predictions to evaluate geometric compatibility at the TOP1-DNA interface were performed using BioCorteX’s proprietary engines version: 20260114_172801. Results: Following sequence-based prioritisation and structural filtering, 13 bacterial proteins predicted to preserve key features of the human TOP1 catalytic core and drug-proximal protein-DNA interface were identified. Across > 2,000 tumour whole-genome sequenced samples, non-small cell lung cancer (NSCLC) demonstrated the highest prevalence of these proteins (24%), significantly exceeding that observed in other epithelial solid tumours, which generally showed low-to-intermediate prevalence (median: 8.3%), and in non-epithelial malignancies (median: 3.4%), where detection was infrequent. This NSCLC-enrichment was not proportional to overall microbial burden. Within NSCLC, substantial geographic heterogeneity was observed across international cohorts, including samples from the United States, United Kingdom, and China, indicating population-level variation in exposure to these structurally relevant bacterial proteins. Conclusions: Building on our prior population-level analyses, these findings support a lung-predominant, tumour microbiome-linked mechanism by which intratumoural bacterial proteins structurally homologous to TOP1 may influence local interactions with TOP1 inhibitors at the tumour site. This framework may contribute to previously observed geographical differences in effective exposure to TOP1-targeted therapies, including TOP1 inhibitor-based chemotherapy and ADCs.