1. Presented by Jacob Miller
Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients
Presented by Jacob Miller

2. Absract
Pre-clinical mouse models suggest the gut microbiome tumor responds to checkpoint immunotherapy but hasn’t been well-characterized in humans.
Melanoma patients’ oral and gut biome were examined while going through anti-PD-1 immunotherapy.
Significant differences of composition and diversity in responders (R) vs non responders (NR)
Metagenomic studies showed functional differences in R
Shows implications for treatment of melanoma patients

3. Reasons
Therapies targeting CTLA-4 and PD-1 proteins are heterogeneous and not durable
Factors beyond the tumor genomics influence therapeutic responses, i.e. gut microbiome
Gut microbiome may influence anti-tumor responses but have not been extensively studied in cancer patients.

4. Methods
Oral and fecal samples where collected from patients undergoing anti-PD- 1 therapy
Blood samples and tumor biopsies were collected and matched pre- treatment
Taxonomic profiling via 16S rRNA gene sequencing and WGS
Patients classified as R or NR via RECIST 1.1

5. Figure 1 Timeline of patient sampling
Phylogenic composition of common bacteria
Inverse Simpson diversity score
Phylogenic composition at family level
KM plot of PFS
Principle coordinate analysis of fecal samples

6. Discussion 1
Found that patients with metastatic melanoma have high diversity microbiomes.
Diversity in the gut microbiome was higher in R patients compared to NR patients
High diversity fecal microbiome had prolong PFS compared to low diversity
Gut microbiome was found to have notable clustering effect, oral did not.

7. Figure 2 Heatmap of OTU abundances Phylogenic composition of OTUs
Taxonomic cladogram from LEfSe
LDA score computed for differentially-abundant taxa in fecal microbiome
Differentially-abundant gut bacteria
Pairwise comparison of abundance of MGS

8. Discussion 2
No significant differences in enrichment were noted in the oral microbiome
Type 1 and Type 2 communities were identified
Type 1: Completely R patients, Clostridiales were enriched
Type 2: Mixture of patients, Bacteroidales were enriched
Showed differentially abundant bacteria in fecal microbiome of R vs NR
Gut microbiome was shown to be relatively stable over time

9. Figure 3
Top: hierarchical clustering of complete linkage. Bottom: stacked bar pot of abundance at order level
Association of community types with response to anit-PD-1
Comparison KM PFS curves
Hierarchical clustering of pathway class enrichment

10. Discussion 3
Begin to focus on Faecalibacterium genis in R and bacteroidales order in NR
Faecalibacterium and prior immunotherapy were used for the multivariate model
Abunance of Faecalibacterium and Bacteroidales outperformed relevant clinical variables in ROC analysis
Next step was to look at the mechanism the gut microbiome may influence response to anit-PD1 therapy

11. Figure 4 Quantification by IHC of the CD8+ cells
Pairwise Spearmen rank correlation heatmap
Univariate linear regression between CD8+ counts
Pairwise Spearman rank correlation heatmap of different fecal taxa
Representative multiplex IHC images
Frequency of various immune cells
Experimental design of studies in GF mice
Difference in size of tumors
Representative tumor growth curves
Quantification of CD8+ density in tumor
Quantification of CD8+ density in gut

12. Discussion 4 Fecal Microbiome Transplant was used in ger free mice
Mice with FMT from R patients had significantly less tumor growth
Responses to anti-PD1 immunotherapy were improved
Faecalilbacterium had higher levels of effector CD4+ and CD8+ T cells
higher density of immune cells

13. Final Discussion/Results
“Favorable” gut microbiome have enhanced anti-tumor immune responses
“Unfavorable” gut microbiomes have impaired anti-tumor immune responses
Warrant evaluation of gut microbiome in cancer patients through clinical trials

14. Reference
Gopalakrishnan, V., Spencer, C. N., Nezi, L., Reuben, A., Andrews, M. C., Karpinets, T. V., … Wargo, J. A. (2018). Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Science (New York, N.Y.), 359(6371), 97–103.