Abstract 1825: A bacterial consortium engineered from feces of patients responding to anti-PD1 treatment mediates tumor response through IFNγ in non-small cell lung cancer

• Published in: Cancer research (Chicago, Ill.) Ill.), 2023-04, Vol.83 (7_Supplement), p.1825-1825
• Main Authors: Newsome, Rachel C., Oh, Joonseok, Jian, Wenya, Gharaibeh, Raad Z., Crawford, Jason, Jobin, Christian
• Format: Article
• Language: English
• ISSN: 1538-7445; 1538-7445
• DOI: 10.1158/1538-7445.AM2023-1825

Introduction: We previously showed that non-small cell lung cancer (NSCLC) patients that respond (R) to immune checkpoint blockade (ICB) have a different microbial community structure than non-responders (NR) pre-treatment (Genome Med 2022). Importantly, we showed that pooled R microbiota transplantation into gnotobiotic xenograft mice decreased tumor growth compared to NR colonized mice following anti-PD1 therapy, a phenomenon associated with enrichment of the Bacteroides genus. However, the bacterial strains driving this synergistic effect with anti-PD1 therapy and mechanism of action are unknown. Method: Feces collected from R mice were used as source material for high-throughput microbial isolation performed with the GALT Prospector technology. Bacterial identification was performed with MALDI-TOF Biotyper and Sanger sequencing. The cell free supernatants and under 3 kDa small molecules of 183 Bacteroides isolates were screened for their ability to stimulate IFNγ production by primary CD8+ T cells by flow cytometry. A consortium composed of 6 IFNγ-stimulating isolates or NR feces was transplanted into a gnotobiotic mouse model of lung cancer treated with anti-PD1, with or without anti-IFNγ monoclonal antibody depletion. Tumors were harvested at endpoint for flow cytometric analysis, and blood serum for IFNγ ELISA. Bioactivity-guided fractionation coupled with LC-MS analysis was used to identify small molecules from the cell free supernatant of a single stimulating Bacteroides isolate. Potential bioactive small molecule characterization was performed using LC-MS/MS supported by computational pipelines for structural prediction followed by NMR for structural confirmation. Results: We cultured and identified 679 isolates from 30 unique species. The cell free supernatant from 6 out of 183 Bacteroides isolates stimulated IFNγ production from primary CD8+ T cells. Small molecules from the six stimulatory isolates’ supernatants significantly induced IFNγ production compared to 6 taxonomy-matched non-stimulatory isolates (P=0.039). A defined consortium composed of the six stimulatory isolates (R-consortium) was able to colonize germ free mice, and decreased tumor growth compared to NR feces-colonized mice (P=0.041). IFNγ depletion of R-consortium mice significantly increased tumor growth (P=0.012) compared to non-depleted mice. Intratumor IFNγ+ CD8+ T cell frequency and circulating serum IFNγ was elevated only in R-consortium mice. Bioassay guided fractionatio