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

Bulk RNA-sequencing (bulk RNA-seq) averages gene expression across cell mixtures, obscuring single-cell heterogeneity and spatial architectures essential for understanding pathological processes. We developed HistoMap, a deep learning-based framework for single-cell spatial deconvolution. The model employs a two-stage pipeline: first, reconstructing high-fidelity single-cell profiles from bulk data using a β-variational autoencoder, and second, utilizing a Histological Vision Transformer (H-ViT) to map these cells to tissue coordinates via dual guidance from transcriptomic references and H&E-stained morphological constraints. HistoMap demonstrated superior performance across diverse human tissues, achieving a Pearson Correlation Coefficient (PCC) of 0.800 on external validation. Application to 14 colorectal cancer cases revealed a Macro_SPP1-mediated desmoplastic barrier. SPP1+ macrophages act as spatial hubs at the invasive front, forming a physical "sequestration belt" that functionally excludes cytotoxic T cells from the tumor core. HistoMap successfully bridges bulk RNA-seq and spatial single-cell architectures. Our findings provide a molecular rationale for immune checkpoint blockade resistance and identify the SPP1-fibroblast axis as a pivotal target for therapeutic sensitization.