Abstract 2207: Intratumoral bacteria predict survival in clear cell renal cell carcinoma (ccRCC)
Authors: Alice C. Martin, Anne-Laure Cattin, Irene Lobon, Zayd Tippu, Fiona Byrne, Charlotte Spencer, Clara Becker, Martha Zepeda Rivera, Krupa Thakkar, Hongui Cha, Angel Fernandez-Sanroman, Annika Fendler, Taja Barber, Leo Bickley, Daqi Deng, Scott Shepherd, Parise Lockwood, Maximiliano Gutierrez, Susan Bullman, Kevin Litchfield, Samra Turajlic
Journal: Cancer Research (2025)

Abstract Background: ccRCC is marked by niches of immune evasion in late-stage disease, that are associated with resistance to immune checkpoint inhibitors (CPI). Intratumoral microbes are emerging as key modulators of the tumor immune microenvironment and may therefore play a yet unrecognised role in ccRCC disease progression and therapy resistance, marking them as potential biomarkers, and novel therapeutic targets. Methods: We extracted bacterial reads from three cohorts of treatment-naïve primary tumors and one cohort of pre- and post-CPI treated tumors: Genomics England Renal (GEL) (636 patients, WGS), TRACERx Renal (154 patients, 629 samples, WGS); TCGA Renal (494 patients, RNA) &amp; ADAPTeR (15 patients, 56 samples, RNA). Bespoke denoising, and decontamination were applied. Live presence of intratumoral bacteria was confirmed through culture and RNAscope. Genera associated with survival were identified using ElasticNet feature selection. Results: We observed significant heterogeneity in bacterial abundance within and across tumors, driven by differences in Cutibacterium abundance. Cutibacterium makes up ∼90% of bacteria in each tumor sample and is enriched in tumors compared to adjacent normal tissue (p=7.1e-10). 9 of 11 colonies grown from two positive tumors were genotyped as Cutibacterium acnes, confirming its live presence and relative abundance in ccRCC tumors. Cutibacterium is higher in late-stage tumors (III&amp;IV) than early-stage tumors (I&amp;II)(p=7.8e-3). Its abundance also separates patients by progression free survival (PFS) and overall survival (OS) (p=9.9e-3, p=0.016) and is higher in CPI non-responders than responders (p=0.028). Association with survival is confirmed in the TCGA cohort independently of stage (PFS = 0.031, OS = 7.3e-4). While other genera associate with survival in either TRACERx or TCGA, only Cutibacterium is prognostic in both. Enrichment analyses of bulk RNA (TRACERx &amp; TCGA), show upregulation of leukocyte taxis and innate immune response with Cutibacterium abundance. To further probe this interaction with the immune microenvironment we are performing single cell spatial transcriptomics, and in vitro co-cultures. Results of these ongoing experiments will be presented at the conference. Conclusions: Cutibacterium either creates or exploits a disease- and CPI-resistance-promoting environment in ccRCC tumors and can therefore act as a prognostic and predictive biomarker. The genus is known for causing chronic inflammation in sebaceous skin follicles, induces Nf-kB signalling, and M2-macrophage differentiation in vitro, and associates with myeloid response in ccRCC tumors. Together this supports a compelling hypothesis that Cutibacterium reduces survival in ccRCC by creating immunosuppressive niches, thereby fostering disease progression and CPI-resistance. Citation Format: Alice C. Martin, Anne-Laure Cattin, Irene Lobon, Zayd Tippu, Fiona Byrne, Charlotte Spencer, Clara Becker, Martha Zepeda Rivera, Krupa Thakkar, Hongui Cha, Angel Fernandez-Sanroman, Annika Fendler, Taja Barber, Leo Bickley, Daqi Deng, Scott Shepherd, Parise Lockwood, Maximiliano Gutierrez, Susan Bullman, Kevin Litchfield, Samra Turajlic. Intratumoral bacteria predict survival in clear cell renal cell carcinoma (ccRCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2207.