Abstract P5-06-26: Gut microbiome profiling of patients with metastatic breast cancer undergoing immune checkpoint inhibitor therapy
Authors: Yuan Yuan , Highlander Sarah , Yost Susan E , Robinson Kim , Padam Simran , Tang Aileen , Martinez Norma , Gillece John , Reining Lauren , Sedrak Mina , Mortimer Joanne , Waisman James 
Published: March 2020

Abstract
Background: Collection of fecal samples is non-invasive, and DNA sequencing of microorganisms can provide a profile of the gut microbiome which may be an indicator of general health and disease, including inflammation, digestive inefficiencies, and the presence of pathogens. The gut microbiome has been associated with response to immune checkpoint inhibitors (ICI) in patients with solid tumors. We aim to study the association of gut microbiome and response to therapy in patients with metastatic breast cancer (BC) undergoing ICI therapies.
Methods: 50 fecal samples from two ICI clinical trials (NCT02971761, N=22; NCT02778685, N=28) were collected at baseline, on treatment and at the end of treatment. DNA was extracted, and 16S rRNA gene libraries were generated targeting the variable region 4 (V4) region of the bacterial and archaeal rRNA gene. Libraries were sequenced on the Illumina MiSeq and sequence reads were analyzed using QIIME2.
Results: A total of 22 dominant taxa (present ≥5% in any one sample) were identified in samples from 12 triple negative BC patients treated with pembrolizumab + GTx-024 (Enobosarm) and 17 dominant taxa were identified taxa 10 ER+ BC patients treated with pembrolizumab, letrozole, and palbociclib. As is true for most microbiome studies, inter-subject variation was much greater than intra-subject variation. However, in some patients there was a significant change in the composition of the microbial communities over time. In the first study, two patients had partial response (PR) to treatment and both had relatively “healthy” gut microbiota dominated by Bacteroides, Faecalibacterium prausnitzii, and other short chain fatty acid producers like Ruminococcus bromii or Roseburia faecis. Most of the patients who progressed had dysbiotic gut microbiomes and four had very high (≥20%) relative abundance of Prevotella copri, an organism associated with inflammation. In the second study, four patients had PR, and as before, these patients had “healthy” gut signatures dominated by Bacteroides and short chain fatty acid-producing Firmicutes. In one of these patients, a high level of Prevotella stercorea (57%)at baseline was replaced by Bacteroides and Lachnospira as treatment proceeded. Three additional patients had very high levels of P. copri (≥34%); one resolved during treatment, the others did not. Shannon’s diversity index was used to measure abundance and evenness in the fecal communities. Several samples in both studies had very low diversity at baseline. In most cases, the diversity increased following treatment.
Conclusion: Most patients who progressed on ICI had dysbiotic gut microbiomes present at baseline and later time points, such as a high relative abundance of Prevotella (implicated in inflammatory processes); this often resolved during therapy. Our observations provide promise for future use of the gut microbiome as a predictor of response to immunotherapy for BC and the potential for modulating the gut microbiome to improve responses in patients with dysbiosis.
Citation Format: Yuan Yuan, Sarah Highlander, Susan E Yost, Kim Robinson, Simran Padam, Aileen Tang, Norma Martinez, John Gillece, Lauren Reining, Mina Sedrak, Joanne Mortimer, James Waisman. Gut microbiome profiling of patients with metastatic breast cancer undergoing immune checkpoint inhibitor therapy [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-06-26.