Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes

Area of Science:

• Oncology
• Microbiology
• Bioinformatics

Background:

• The tumor microbiome is crucial for cancer progression and treatment response.
• Understanding microbial presence within tumor cells is essential.

Purpose of the Study:

• To develop and validate a computational pipeline (CSI-Microbes) for microbial analysis in single-cell RNA sequencing (scRNA-seq) data.
• To systematically evaluate scRNA-seq technologies for microbial recovery.
• To investigate microbial co-occurrence and host cell interactions in carcinomas.

Main Methods:

• Development of the CSI-Microbes computational pipeline.
• Systematic evaluation of multiple scRNA-seq technologies for microbial unique molecular identifier recovery.
• Analysis of patient esophageal and colorectal carcinoma samples.

Main Results:

• 10x Genomics chemistries (3' v3 and 5') showed superior microbial recovery.
• Distinct microbial genera co-occur within host cells, suggesting intracellular interactions.
• Microbial RNA is enriched in myeloid cells expressing proinflammatory cytokines (e.g., IL1Β, CXCL8).
• Tumor cells up-regulate antigen processing and presentation pathways upon infection.

Conclusions:

• Myeloid cells containing engulfed bacteria are a significant source of bacterial RNA in the tumor microenvironment (TME).
• These myeloid cells may promote TME inflammation and influence immunotherapy outcomes.