942 The tumor microbiome correlates with response to immune checkpoint inhibitors in renal cell carcinoma

Abstract

BackgroundImmune checkpoint inhibitor therapy, or ICI, is currently the most successful treatment option for patients with renal cell carcinoma (RCC). However, only 20% of patients have a durable response,1 driving a significant need to improve treatment outcomes. The tumor microbiome has recently been shown to play a role in chemotherapy-based treatment outcomes, but, to our knowledge, no study has explored its role in response to ICIs.2–4MethodsTumor samples were collected from 22 patients with RCC as a part of the Total Cancer Care program at The Ohio State University Comprehensive Cancer Center. Raw RNA-seq reads from these biopsies, as well as data on the responses to ICI therapy were collected. Response evaluation was based on RECIST v1.1 criteria with complete or partial response, or stable disease classified as ”Responders,”, and progressive disease classified as ”Non-responsders”. The RNA-seq reads were processed through a pipeline developed by the Spakowicz lab, known as ExoTIC (Exogenous sequences in Tumor and Immune Cells), to carefully identify exogenous sequences.5 6 Reads that don’t align to the human reference genome are meticulously filtered of (1) common laboratory contaminants, (2) taxa that inversely correlate with input RNA quantity, and (3) taxa commonly found in the negative controls of microbiome experiments. DESeq2 was used to perform a differential abundance analysis on the comparison groups at every taxonomic level.ResultsThe 22 patients with RCC range from 22 to 74 years of age at diagnosis, are 72.7% male, and 54.5% responded to ICIs. Exogenous taxa are identified in the tumor RNAseq, including bacteria, fungi, and viruses (figure 1). Within the tumors responsive to immunotherapy, there was found to be a significant enrichment of certain microbial species, including Bacillus thuringiensis, Comamonas testosteroni, Colletotrichum higginsianum, and Elaeis guineesis. Comparatively, the cohort of non-responsive tumors was found to have a significant enrichment of Candidatus Promineofilum breve, Clostridioides difficile, Nocardia cyriacigeorgica, Streptomyces sp. CdTB01, and Streptomyces venezuelae (figure 2).Abstact 942 Figure 1Relative abundances of exogenous taxa found in tumor RNAseq are shown in a stacked bar plotAbstact 942 Figure 2Differential abundance analysis of taxa found within tumor RNAseq data by the exotic pipeline. Colored points represent significantly (pvalue < 0.05) enriched taxa with a high (>2.5) fold-difference in abundance between the groupsConclusionsWe found that prior to ICI treatment the tumor microbiome of patients with RCC whose tumors responded to immunotherapy vary from those that did not respond to treatment. This implies that a therapeutic target to modify the tumor microbiome to improve treatment outcomes. Future research will evaluate whether these correlations are causally associated with outcomes and will evaluate their effect on the tumor microenvironment including immune cell infiltration.AcknowledgementsThe authors acknowledge the support and resources of the Ohio Supercomputing Center (PAS1695).ReferencesCiccarese C, Di Nunno V, Iacovelli R, Massari F. Future perspectives for personalized immunotherapy in renal cell carcinoma. Expert opinion on biological therapy. 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Science 2020 May 29;368(6494):973–980.Poore GD, Kopylova E, Zhu Q, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf J, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Knight R. Microbi-ome analyses of blood and tissues suggest cancer diagnostic approach. Nature 2020;579(7800):567–574. PMID: 32214244.Malalur, Pannaga, Mo, Xiaokui, Hoyd, Rebecca, Hays, John, Carbone, David, Spakowicz, Daniel. Investigating intra-tumor microbes, blood microbes, and CEA for development of non-invasive biomarkers in colorectal cancer. Journal of Clinical Oncology 2021;39(15_suppl): 3551–3551.Malalur PG, Mo X, Hoyd R, Carbone DP, Spakowicz D. Intra-tumoral microbes and overall survival in colorectal cancer patients. Journal of Clinical Oncology 2020;38(15_suppl):4083–4083.Ethics ApprovalData were obtained through an IRB-approved Honest Broker protocol (2015H0185) supporting the Total Cancer Care protocol 2013H0199.

Intratumor bacteria is associated with prognosis in clear-cell renal cell carcinoma

“…Our study encompassed thus far the largest number of ccRCC cases subject to ITB detection. In comparison to previous smaller studies 14–17 , several ITB features appeared to be ubiquitously present at high relative abundance including Proteobacteria and Firmicutes at phylum level and Pseudomonas , Acinetobacter and Staphylococcus at genus level. Lack of difference in ITB loads, composition or diversity between normal and cancer tissue was one of our major findings.…”

“…Clear-cell renal cell carcinoma (ccRCC) is the most common type of malignancy in kidney that is conventionally accepted as sterile organ and ccRCC is expected to harbor a low biomass of ITB. To date, the existing literature on ITB in ccRCC is limited to three full papers [14][15][16] and one meeting proceeding 17 . These studies suffer from small sample sizes, lack of racial diversity, use of a single sequencing technology, and inadequate decontamination process.…”

Resident Microbiome of Kidney Tumors

“…On the other hand, tumors in patients who did not respond to checkpoint inhibitor therapy exhibited enrichment of species including Candidatus Promineofilum breve , Clostridioides difficile, Nocardia cyriacigeorgica, Streptomyces sp. CdTB01 , and Streptomyces venezuelae [ 31 ]. Based on these results, it can be speculated that the composition of the tumor microbiome may predict the effectiveness of therapeutic responses, alongside currently used markers.…”