Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma

• Published in: Genome medicine Vol. 13; no. 1; pp. 160 - 11
• Main Authors: Usyk, Mykhaylo, Pandey, Abhishek, Hayes, Richard B, Moran, Una, Pavlick, Anna, Osman, Iman, Weber, Jeffrey S, Ahn, Jiyoung
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 13-10-2021; BioMed Central; BMC
• Subjects: Adenosine; Algorithms; Analysis; Bacteroides; Bacteroides - genetics; Bacteroides - physiology; Bacteroides dorei; Bar codes; Bioinformatics; Biomarkers; Biomarkers, Tumor; Care and treatment; Clustering; CTLA-4 protein; DNA sequencing; Drug therapy; Feces; Feces - microbiology; Gastrointestinal Microbiome - genetics; Gastrointestinal Microbiome - physiology; Genomes; Humans; Immune checkpoint; Immune Checkpoint Inhibitors; Immune-related adverse events; Immunotherapy; Inflammatory bowel disease; Intestinal microflora; Ipilimumab; Laboratories; Medical care; Medical research; Medicine, Experimental; Melanoma; Melanoma - immunology; Melanoma - therapy; Metagenome; Metagenomics; Metastases; Metastasis; Microbiome; Microbiomes; Patients; PD-1 protein; Prospective Studies; Quality management; Risk groups; RNA; RNA, Ribosomal, 16S; rRNA 16S; Survival; Survival analysis; Taxonomy; Toxicity; Immune-related adverse events; Toxicity; Melanoma; Biomarkers; Prospective design; Survival; Microbiome
• ISSN: 1756-994X; 1756-994X
• DOI: 10.1186/s13073-021-00974-z

Immune checkpoint blockade (ICB) shows lasting benefits in advanced melanoma; however, not all patients respond to this treatment and many develop potentially life-threatening immune-related adverse events (irAEs). Identifying individuals who will develop irAEs is critical in order to improve the quality of care. Here, we prospectively demonstrate that the gut microbiome predicts irAEs in melanoma patients undergoing ICB.
Pre-, during, and post-treatment stool samples were collected from 27 patients with advanced stage melanoma treated with IPI (anti-CTLA-4) and NIVO (anti-PD1) ICB inhibitors at NYU Langone Health. We completed 16S rRNA gene amplicon sequencing, DNA deep shotgun metagenomic, and RNA-seq metatranscriptomic sequencing. The divisive amplicon denoising algorithm (DADA2) was used to process 16S data. Taxonomy for shotgun sequencing data was assigned using MetaPhlAn2, and gene pathways were assigned using HUMAnN 2.0. Compositionally aware differential expression analysis was performed using ANCOM. The Cox-proportional hazard model was used to assess the prospective role of the gut microbiome (GMB) in irAES, with adjustment for age, sex, BMI, immune ICB treatment type, and sequencing batch.
Two natural GMB clusters with distinct community compositions were identified from the analysis of 16S rRNA data (R
= 0.16, p < 0.001). In Cox-proportional hazard modeling, these two clusters showed a near 7-fold differential risk for developing irAEs within 1 year of initiating treatment (HR = 6.89 [95% CI: 1.33-35.58]). Using shotgun metagenomics, we further identified 37 bacterial strains differentially expressed between the risk groups, with specific dominance of Bacteroides dorei within the high-risk GMB cluster and Bacteroides vulgatus in the low-risk cluster. The high-risk cluster also appeared to have elevated expression of several functional pathways, including those associated with adenosine metabolism (all FDR < 0.05). A sub-analysis of samples (n = 10 participants) at baseline and 6 and 12 weeks after the start of treatment revealed that the microbiome remained stable over the course of treatment (R
= 0.88, p < 0.001).
We identified two distinct fecal bacterial community clusters which are associated differentially with irAEs in ICB-treated advanced melanoma patients.