Intratumoral microbiome composition and its role in tumor recurrence in primary liver cancer

The human microbiome is increasingly recognized as a factor in cancer development, though its role in primary liver cancer (PLC) remains unclear. This retrospective cohort study examines tissue-specific microbiota differences between hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), and explores their association with tumor recurrence in PLC.

Clinical data from 116 patients (85 HCC and 31 age-matched CCA) were analyzed. Fresh frozen samples underwent RNAscope™ ISH assay for microbial RNA detection, while the MiSeq platform targeted 16 S ribosomal RNA. Microbiome functional pathways were explored with Tax4Fun2, and predictors of recurrence were identified through logistic regression analysis.

Microbial RNA was detected within liver sinusoids, the basal lamina of intrahepatic bile ducts, and hepatocyte cytosol. 16 S ribosomal RNA analysis revealed differences in microbiome composition, including a distinct Firmicutes/Bacteroidetes ratio between CCA and HCC patients. Specific functional pathways were differentially enriched between the two groups. LEfSe and logistic regression analyses identified Aquabacterium spp. as a potential marker for HCC recurrence (OR, 14.77; 95 % CI, 1.07-203.94; p = 0.044). Increased abundances of Brevundimonas spp. (OR, 3.1 E+17; 95 % CI, 4.3 E+3-2.2 E+31; p = 0.013), Novosphingobium spp. (OR, 3.5 E+20; 95 % CI, 4.4 E+5-2.8 E+35; p = 0.007), and Pelomonas spp. (OR, 3.3 E+21; 95 % CI, 3.0 E+8-3.5 E+34; p = 0.001), along with decreased Staphylococcus spp. (OR 0.00; 95 % CI, 0.00-0.06; p = 0.003), were independent predictors of CCA occurrence.

This study reveals that intratumoral microbiota help distinguish PLC subtypes and are associated with recurrence, identifying Aquabacterium as a potential marker for HCC recurrence and microbiome-based management.