Primary resistance to ICI-based regimens is associated with early longitudinal changes in the fecal microbiome and loss of microbial stability

While immune checkpoint inhibitors (ICI)-based regimens and chemo-immunotherapy combinations (chemo-ICI) are now first-line therapy for patients with metastatic non-small cell lung cancer (NSCLC), the number of patients who experience a sustained response to treatment remains limited. The majority of patients will not benefit from initial treatment (primary resistance) or develop progressive disease after an initial period of response (acquired resistance). Microbiome-based biomarkers offer an opportunity to identify patients who may have a poor response to ICI-based regimens using non-invasive methods, and potentially, then the microbiota may be amenable to therapy-enhancing alteration. However, a deep understanding of the longitudinal dynamics of gut microbial features in patients treated with ICIs in NSCLC, a feature of likely importance for microbiome-based therapeutics, remains limited. In this study, we show that patients with NSCLC who experience primary resistance to an ICI-based regimen show a loss of intra-individual microbiome stability in the first 4 months during treatment with an ICI-based regimen, independent of antibiotic exposure. Loss of microbiome stability was validated in a second tumor type in patients with melanoma. To identify key microbial species associated with progression, recursive feature elimination with random forest classifiers was used to identify temporally associated microbial species associated with disease progression. An index of these progression-associated species was able to predict clinical outcomes based on pre-treatment fecal samples, with further validation on an independent cohort. Together, our data show that microbial instability may be an early indicator of ICI-resistance in patients with NSCLC and melanoma, with the potential to be developed into biomarkers of primary resistance to ICI-based regimens.