Tumor-associated microbiota are an important component of the tumor microenvironment (TME) across 33 human cancers. However, little evidence is available regarding the spatial distribution and localization of these microbes in tumor cells.
Addressing this research gap is recent nature A periodical study evaluated the spatial, cellular, and molecular interactions of the microbiota in oral squamous cell carcinoma (OSCC) and colorectal carcinoma (CRC). In this study, the scientists mapped the cellular-bacterial, spatial, and molecular interactions within the TME using single-cell RNA sequencing (scRNA-seq) and On site spatial profiling techniques.
Cancer patients’ tumors usually consist of malignant cells surrounded by a complex network of non-malignant cells. These cells may exhibit pro- or anti-tumor effects depending on their abundance and type. Both in the laboratory And the in vivo Experiments indicated the presence of bacteria in the tumor-associated microbiota, which play an important role in cancer development, immune surveillance, metastasis, and chemoresistance. Molecular analysis and bioimaging data also demonstrated the presence of intratumoral microbiota across major cancer types.
There is a lack of evidence regarding the specific identity of host cells through which tumour-associated microbes interact with tumor cells of cancer patients. In addition, little evidence regarding the identification of specific cells harboring organisms has been documented. The influence of the subtle cellular interactions between host and microbes and the spatial distribution of microbes within the tumor on their functional capacities within the TME is unclear.
About the study
16S rRNA gene sequencing of the tumoral tissues of CRC patients indicated the presence of various bacteria, including spindle. The abundance of these bacteria differed among CRC patients. Dendrogram and principal components analysis with beta diversity cohort indicated that the majority of cancer patients had relatively stable microbiome compositions. However, most patients showed varying degrees of heterogeneity in the composition of the microbiome within the tumor.
The RNAscope- fluorescence On site Hybridization imaging (RNAscope-FISH) confirmed the heterogeneous spatial distribution of bacterial communities in the TME. Data based on RNAscope-FISH showed that there is spindle Nucleuswhich was validated by microbiome analysis and quantitative polymerase chain reaction technology.
The 10x Visium spatial transcriptome was also used to detect and analyze the spatial distribution of microbes within the tumor of CRC and OSCC samples. This approach identified 28% of the stains captured within OSCC tumors and 46% of CRC tumors.
aHaematoxylin and eosin (H&E) staining (left), spatial distribution of total bacterial reads (center) and total UMI transcripts (right) throughout tumor tissues in 10x Visium capture slides from human OSCC and CRC specimens. Bpie chart of the top 10 dominant bacterial genera detected in 10x Visium RNA sequencing data from OSCC and CRC tumors. cRNAscope-FISH imaging showing the distribution of bacteria across tumor tissue in a serial slide after 10x Visium section. F. Probe cores are F. Scale bars, 1 mm. DrSpatial distribution of Parvimonas, Peptoniphilus, and Fusobacterium UMIs detected in 10x Visium OSCC sample data. eand the spatial distribution of Fusobacterium, Bacteroidetes, and Leptotrichia UMIs detected in 10x Visium CRC sample data.
in an OSCC tumor, ParphemonasAnd the peptonephilusAnd the spindle Dominant strains were found, while spindle And the Bacteroides The tumor races were dominant in CRC.
The 10x Visium spatiotemporal technology enabled the direct detection, quantification and spatial mapping of viable bacteria within healthy tumor tissues of cancer patients. It also indicated the complexity of the interactions of microbes within the tumor across the tumor tissue.
The GeoMx digital spatial profiling platform (DSP) helped determine the expression profile of 77 proteins associated with cancer development and anti-tumor immunity. This technique, together with RNAscope and immunohistochemistry (IHC) approaches, indicated that bacterial communities inhabit very fine sutures that are immunosuppressive and not highly vascular. In addition, bacterial strains tend to inhabit malignant cells with low levels of Ki-67.
The INVADEseq (Invasion- and Adhesion-Directed Expression Sequencing) technique was developed to evaluate the bacterial host-cell-cell interaction within the TME and the effect on host-cell transcription. This technique is associated with the insertion of a primer to target conserved regions of bacterial 16S rRNA. Subsequently, libraries (cDNA) with bacterial transcripts can be produced from human cells associated with bacteria. A critical aspect of this method is that primer insertion does not affect the gene expression profile of human CRC cells.
The INVADEseq technique was validated using the human CRC cell line HCT116 that was infected with two bacterial species, namely: F. NucleusAnd the Porphyromonas gingivalisAnd the Intermediate Prevotella. enabled the mapping of bacterial populations in single human cells. Importantly, INVADEseq confirmed a role F. Nucleus And the s. gums in affecting the heterogeneity of cancer cells. These bacterial strains alter distinct transcriptional programs that aid in specific cell clustering. Alteration of transcriptional pathways is also associated with manifestations of inflammation, cell dormancy, metastasis, and DNA repair.
The present study revealed that tumor cells infected with bacteria affect their surroundings as a single cell, which subsequently recruits myeloid cells to the bacterial zone. Notably, the microbiome present within the tumor was not a random phenomenon. Instead, the presence of bacteria within a tumor has been argued to be a highly regulated process in microniches with immune and epithelial cell functions affecting cancer development.
Although the current study focused on two types of cancer, the tools and techniques can be used to study all major cancer types and those with microbes within the tumor.