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Related Concept Videos

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Related Experiment Video

Updated: Jan 15, 2026

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 summary is machine-generated.

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.