Robinson, W;
Stone, JK;
Schischlik, F;
Gasmi, B;
Kelly, MC;
Seibert, C;
Dadkhah, K;
... Ruppin, E; + view all
(2024)
Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes.
Science advances
, 10
(27)
, Article eadj7402. 10.1126/sciadv.adj7402.
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Abstract
The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data and for analyzing differential abundance of taxa. Using a series of controlled experiments and analyses, we performed the first systematic evaluation of the efficacy of recovering microbial unique molecular identifiers by multiple scRNA-seq technologies, which identified the newer 10x chemistries (3' v3 and 5') as the best suited approach. We analyzed patient esophageal and colorectal carcinomas and found that reads from distinct genera tend to co-occur in the same host cells, testifying to possible intracellular polymicrobial interactions. Microbial reads are disproportionately abundant within myeloid cells that up-regulate proinflammatory cytokines like IL1Β and CXCL8, while infected tumor cells up-regulate antigen processing and presentation pathways. These results show that myeloid cells with bacteria engulfed are a major source of bacterial RNA within the tumor microenvironment (TME) and may inflame the TME and influence immunotherapy response.
| Type: | Article |
|---|---|
| Title: | Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1126/sciadv.adj7402 |
| Publisher version: | https://doi.org/10.1126/sciadv.adj7402 |
| Language: | English |
| Additional information: | Copyright © 2024 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). |
| Keywords: | Humans, Single-Cell Analysis, RNA-Seq, Bacteria, Tumor Microenvironment, Myeloid Cells, Sequence Analysis, RNA, Colorectal Neoplasms, Computational Biology, RNA, Bacterial, Esophageal Neoplasms, Microbiota, Single-Cell Gene Expression Analysis |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Oncology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10194731 |
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