Intratumor microbiome features reveal antitumor potentials of intrahepatic cholangiocarcinoma

Abstract

Intrahepatic cholangiocarcinoma (ICC) is a rare malignancy with a high prevalence in China. This study aimed to characterize the ICC tissues’ bacterial metagenomics signature and explore its antitumor potential for cancer. In this study, 16S rRNA sequencing was carried out on 99 tissues to characterize the features of intratumoral microbiota, followed by single-cell RNA sequencing (scRNA-seq) and multilevel validation. The presence of microbial DNA in tissues was determined using staining, fluorescence in situ hybridization (FISH), and transmission electron microscopy (TEM). A Gram-positive aerobic bacterium, identified as Staphylococcus capitis , was cultured from fresh tissues. Meanwhile, scRNA-seq showed that intratumoral bacteria could be present in multiple cell types. Using 16S rRNA sequencing, we identified a total of 2,320,287 high-quality reads corresponding to 4,594 OTU (operational taxonomic units) sequences. The most abundant bacterial orders include Burkholderiales, Pseudomonadales, Xanthomonadales, Bacillales and Clostridiales . Alpha and Beta diversity analysis revealed specific features in different tissues. In addition, the content of Paraburkholderia fungorum was significantly higher in the paracancerous tissues and negatively correlated with CA199 (Carbohydrate antigen199) levels. The results of in vitro and in vivo experiments suggest that P. fungorum possesses an antitumor activity against tumors. Metabolomics and transcriptomics showed that P. fungorum could inhibit tumor growth through alanine, aspartate and glutamate metabolism. We determined the characteristic profile of the intratumoral microbiota and the antitumor effect of P. fungorum in ICC.

Host–microbiota interaction during cancer progression from bulk to single‐cell level

“…Some bacterial species have antitumour activity against tumours, such as Paraburkholderia fungorum, which inhibits tumour growth mainly through the regulation of alanine, aspartate and glutamate metabolism. 27 In contrast, the intestinal estrogen receptor beta can impede the progression of CRC by mediating the formation of beneficial microbiota. 31 Microbiome dysbiosis contributes significantly to carcinogenesis on a number of levels, including immunological, inflammatory and metabolic pathways.…”

“…It has been indicated that the microbial composition is generally similar between tumours and adjacent tissues, possibly suggesting the temporal and spatial features of microbial ecosystems. 27,28 Cancer cells infected by bacteria are able to invade the surrounding area as a single cell and can also attract myeloid cells to the bacterial region. 3 The recruitment of myeloid cells can be observed in GC.…”

Intratumor microbiome: selective colonization in the tumor microenvironment and a vital regulator of tumor biology

“…The intratumor microbiome can also modulate the tumor biology via influencing metabolism. In intrahepatic cholangiocarcinoma, the intratumor microbiota Paraburkholderia fungorum was significantly enriched in paracancerous tissues, which could inhibit tumor growth through alanine, aspartate, and glutamate metabolism 91 . And in breast cancer, integrating bulk and single‐cell RNA sequencing data revealed that the intratumor microbiome was significantly associated with metabolic heterogeneity in breast cancers, highlighting the need for further mechanistic investigations 92 .…”

Dynamic interplay of intratumoral microbiota within the colorectal cancer microenvironment

“…CRC tissues are notable for their higher bacterial and fungal load in comparison to healthy tissue, with particular bacterial strains enriched within the tumor. 22 The intratumoral microbiota in CRC can be attributed to three primary sources. 23,24 First, the mucosal barrier of the colon, which naturally houses diverse microorganisms, becomes a conduit for these microbes during instances of mucosal damage caused by tumor development.…”

“…CRC tissues are notable for their higher bacterial and fungal load in comparison to healthy tissue, with particular bacterial strains enriched within the tumor 22 …”