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Related Concept Videos

The Tumor Microenvironment02:17

The Tumor Microenvironment

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Every normal cell or tissue is embedded in a complex local environment called stroma, consisting of different cell types, a basal membrane, and blood vessels. As normal cells mutate and develop into cancer cells, their local environment also changes to allow cancer progression. The tumor microenvironment (TME) consists of a complex cellular matrix of stromal cells and the developing tumor. The cross-talk between cancer cells and surrounding stromal cells is critical to disrupt normal tissue...
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Related Experiment Video

Updated: Sep 19, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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SpaLinker identifies phenotype-associated spatial tumor microenvironment features by integrating bulk and spatial

Xiaojie Cheng1, Chen Tang2, Kejing Dong2

  • 1Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Reproductive Medicine Center, Department of Obstetrics and Gynecology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China.

Cell Genomics
|June 6, 2025
PubMed
Summary

SpaLinker links spatial transcriptomics data to clinical outcomes by analyzing tumor microenvironments. This computational framework identifies prognostic spatial features across diverse cancers, enhancing spatial sequencing

Keywords:
SpaLinkerclinical phenotypespatial transcriptomicstertiary lymphoid structuretumor microenvironmenttumor-normal interface

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Author Spotlight: Multiplex Immunofluorescence Combined with Spatial Image Analysis for the Clinical and Biological Assessment of the Tumor Microenvironment
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Area of Science:

  • Oncology
  • Genomics
  • Bioinformatics

Background:

  • Spatial transcriptomics (ST) reveals tumor microenvironment (TME) complexity.
  • Linking spatial data to clinical phenotypes is challenging due to limited annotations.

Purpose of the Study:

  • Introduce SpaLinker, an integrated framework for analyzing ST data.
  • Decipher spatially resolved TMEs at molecular, cellular, and structural levels.
  • Assess prognostic significance of spatial features using bulk RNA sequencing (RNA-seq) data.

Main Methods:

  • Developed a phenotype-driven computational framework.
  • Integrated ST data with bulk RNA-seq data.
  • Applied SpaLinker to diverse pan-cancer ST datasets.

Main Results:

  • SpaLinker effectively recognizes spatial architectures like tertiary lymphoid structures and tumor-normal interfaces.
  • Identified links between spatial features and distinct clinical outcomes.
  • Demonstrated utility and effectiveness in diverse tumor ST datasets.

Conclusions:

  • SpaLinker is a valuable pan-cancer analytical platform.
  • Enables de novo identification of phenotype-associated spatial TME features.
  • Significantly enhances the clinical utility of spatial sequencing technology.