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Cancer-Associated Fibroblasts from Mouse Mammary Tumors as Tools for Molecular and Computational Studies
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SMTdb: A Comprehensive Spatial Meta-Transcriptome Resource in Cancer.

Weiwei Zhou1,2, Qingyi Yang2, Jiyu Guo2

  • 1College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.

Molecular Biology and Evolution
|October 15, 2025
PubMed
Summary

This study maps the cancer microbiome using spatial transcriptomics, revealing microbial distribution and interactions within tumors. The new database provides insights into the tumor microenvironment and host-gene associations.

Keywords:
databaseimmune cellsmicrobiotasingle-cell omicsspatially resolved transcriptomicstumor microenvironment

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Area of Science:

  • Oncology
  • Microbiology
  • Bioinformatics

Background:

  • Microorganisms are found in tumors, but their spatial distribution is poorly understood.
  • Spatial transcriptomics allows mapping cellular and microbial transcripts at high resolution.
  • Investigating the cancer microbiome spatially is crucial for understanding tumor biology.

Purpose of the Study:

  • To create a comprehensive spatial meta-transcriptome resource for cancer.
  • To build a database (SMTdb) detailing microbial abundance, distribution, and TME enrichment.
  • To enable exploration of microbiota-host interactions in the tumor microenvironment.

Main Methods:

  • Manual curation of 203 fresh frozen tumor slices across 20 cancer types.
  • Integration of spatial transcriptomic data from 334,253 spots and 1,908,646 cells.
  • Construction of the spatial meta-transcriptome database (SMTdb).

Main Results:

  • Detailed insights into the abundance, distribution, and TME-enriched regions of 1,218 microbiota.
  • Identification of host gene modules associated with specific microbiota.
  • Data on microbiota-immune cell co-occurrence within the tumor microenvironment.

Conclusions:

  • The developed atlas resource provides a structured platform for cancer microbiome research.
  • Facilitates investigation of microbial ecosystem and host interactions in cancer.
  • Enables deeper understanding of the spatial dynamics of the tumor microbiome.