INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level...

Area of Science:

• Microbiology
• Genomics
• Cancer Research

Background:

• Single-cell RNA sequencing (scRNAseq) is crucial for understanding tumor microenvironment heterogeneity.
• Standard scRNAseq methods often miss bacteria in tumors due to lack of poly(A) tails in bacterial RNA.
• Intratumoral bacteria are increasingly recognized as significant components of the tumor microenvironment.

Purpose of the Study:

• To develop a scRNAseq method capable of simultaneously profiling host and microbial RNA within single cells.
• To identify bacterial presence within specific human cell types in tumors.
• To investigate host transcriptional responses to intratumoral bacteria.

Main Methods:

• Adaptation of the 10x Genomics 5' scRNAseq protocol with an added primer targeting bacterial 16S ribosomal RNA.
• Simultaneous generation of eukaryotic and bacterial RNA libraries at single-cell resolution.
• Application of the INVADEseq method to human cancer cell lines and patient tumor specimens.

Main Results:

• INVADEseq successfully detected and identified intracellular bacteria within human cells in tumor samples.
• The method quantified the proportion of human cells harboring bacteria.
• INVADEseq revealed host transcriptional programs modulated by the presence of associated bacteria.

Conclusions:

• INVADEseq is a reliable tool for simultaneously analyzing host and microbial single-cell transcriptomes in tumors.
• This method enhances the understanding of host-microbe interactions within the tumor microenvironment.
• INVADEseq provides novel insights into the role of bacteria in cancer biology.