A comprehensive study of intratumor bacteria in clear-cell renal cell carcinoma identifies Cutibacterium acnes as a protector via suppression of macrophage M2 polarization.

UNLABELLED: Intratumor bacteria (ITB) have emerged as key modulators in various malignancies; however, their role in clear-cell renal cell carcinoma (ccRCC) remains unclear and elusive. In this study, we analyzed seven independent cohorts (comprising one 16S rRNA sequencing and six bulk RNA sequencing data sets) encompassing 517 ccRCC and 65 paired adjacent normal tissues. Following a rigorous decontamination pipeline, we found that neither microbial diversity nor compositional profiles differed significantly between cancerous and adjacent normal tissues. Thirteen specific genera-including Streptococcus, Rothia, Cutibacterium, and Corynebacterium-exhibited significant prognostic associations. The microbial risk scores constructed from these genera demonstrated robust performance in prognostic risk stratification and were validated as an independent prognostic factor for both overall survival and progression-free survival, respectively. Host-microbe interaction analysis revealed correlations between these prognostic genera and oncogenic pathways, particularly those involved in immune regulation and metabolism. Notably, culturomics successfully isolated Cutibacterium acnes (C. acnes) from ccRCC tissues, and higher C. acnes' abundance was correlated with a favorable prognosis. Functional assays revealed that C. acnes inhibits tumor growth and suppresses macrophage M2 polarization. Mechanistically, C. acnes and its primary metabolite, propionic acid, attenuate macrophage M2 polarization by activating TNF signaling. Our findings underscore the protective role of C. acnes in the ccRCC microenvironment and highlight its potential as a target for precision immunotherapy.

IMPORTANCE: To address previous methodological limitations, we applied rigorous decontamination to multi-omic datasets to isolate and experimentally validate intratumor bacteria colonization in ccRCC. Comparable profiles between tumorous and normal tissues suggest intratumor bacteria generally act as "passengers." We successfully constructed robust microbial risk scores predictive of patient survival. Mechanistically, in vitro and in vivo models demonstrated that Cutibacterium acnes and its metabolite, propionic acid, inhibit tumor growth and suppress M2 macrophage polarization via TNF signaling. These findings highlight the protective role of Cutibacterium acnes in the tumor microenvironment, revealing it as a promising target for precision immunotherapy.