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Related Experiment Video

Updated: Jun 27, 2026

Dissociation of Human and Mouse Tumor Tissue Samples for Single-cell RNA Sequencing
05:58

Dissociation of Human and Mouse Tumor Tissue Samples for Single-cell RNA Sequencing

Published on: August 16, 2024

HistoMap: Reconstructing Spatially Resolved Single-Cell Profiles from Bulk RNA-Seq to Decipher the Immune-Excluded

Jia He1, Yong Cao1, Yan Liu1

  • 1Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin 150081, China.

International Journal of Molecular Sciences
|June 26, 2026
PubMed
Summary

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This summary is machine-generated.

HistoMap, a deep learning tool, reconstructs single-cell spatial data from bulk RNA sequencing. It reveals a SPP1-mediated barrier in colorectal cancer, impacting T cell exclusion and offering therapeutic targets.

Area of Science:

  • Computational Biology
  • Genomics
  • Pathology

Background:

  • Bulk RNA sequencing (RNA-seq) averages gene expression, masking crucial single-cell heterogeneity and spatial information.
  • Understanding cellular spatial architecture is vital for deciphering pathological processes.

Purpose of the Study:

  • To develop a deep learning framework, HistoMap, for single-cell spatial deconvolution from bulk RNA-seq data.
  • To map single cells to tissue coordinates using transcriptomic and morphological data.
  • To investigate the spatial architecture of colorectal cancer and its implications for immunotherapy.

Main Methods:

  • A two-stage deep learning pipeline: β-variational autoencoder for single-cell profile reconstruction and a Histological Vision Transformer (H-ViT) for spatial mapping.
Keywords:
SPP1+ macrophagescolon cancerhistology–transcriptomic integrationimmune-excluded phenotypesingle-cell reconstructiontumor microenvironment

Related Experiment Videos

Last Updated: Jun 27, 2026

Dissociation of Human and Mouse Tumor Tissue Samples for Single-cell RNA Sequencing
05:58

Dissociation of Human and Mouse Tumor Tissue Samples for Single-cell RNA Sequencing

Published on: August 16, 2024

  • Dual guidance using transcriptomic references and H&E-stained morphological features.
  • Validation across diverse human tissues and application to 14 colorectal cancer cases.

    • Main Results:

    • HistoMap achieved high performance with a Pearson Correlation Coefficient (PCC) of 0.800 on external validation.
    • Identified a Macro_SPP1-mediated desmoplastic barrier in colorectal cancer.
    • Revealed SPP1+ macrophages forming a 'sequestration belt' excluding cytotoxic T cells from the tumor core.

    Conclusions:

    • HistoMap effectively bridges bulk RNA-seq with spatial single-cell data, enabling detailed spatial architecture reconstruction.
    • The SPP1+ macrophage barrier offers a molecular explanation for immune checkpoint blockade resistance.
    • The SPP1-fibroblast axis presents a potential therapeutic target for enhancing cancer immunotherapy sensitization.