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<p>Tissues are organized through the assembly of diverse cell types into multicellular structures that exhibit hierarchical spatial organization. We present HRCHY-CytoCommunity, a graph neural network framework for identifying multi-level tissue structures directly from cell-type annotated spatial maps. It integrates differentiable graph pooling, adaptive edge pruning, and consistency and balance regularization in an end-to-end model, simultaneously inferring robust structures across multiple scales while preserving complete cellular coverage and fully nested relationships. The framework also supports cross-sample hierarchy alignment via cell-type enrichment-based clustering. Benchmarking on diverse spatial omics datasets, HRCHY-CytoCommunity outperforms existing hierarchical and non-hierarchical methods in identifying both coarse-grained tissue compartments and fine-grained cellular neighborhoods. Applied to a breast cancer cohort with clinical outcomes, the framework enables hierarchical prognostic stratification of patients and reveals survival-associated spatial patterns. HRCHY-CytoCommunity represents a general and scalable tool for deciphering tissue organization from single cells to multicellular modules, and ultimately to intact tissues and organs.</p>

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HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年2月28日

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  • Runzhi Xie,
  • Zekun Wang,
  • Jianrui Liu,
  • Han Xu,
  • Yafei Xu,
  • Jiadong Lin,
  • Yuxuan Hu,
  • Lin Gao

摘要

Tissues are organized through the assembly of diverse cell types into multicellular structures that exhibit hierarchical spatial organization. We present HRCHY-CytoCommunity, a graph neural network framework for identifying multi-level tissue structures directly from cell-type annotated spatial maps. It integrates differentiable graph pooling, adaptive edge pruning, and consistency and balance regularization in an end-to-end model, simultaneously inferring robust structures across multiple scales while preserving complete cellular coverage and fully nested relationships. The framework also supports cross-sample hierarchy alignment via cell-type enrichment-based clustering. Benchmarking on diverse spatial omics datasets, HRCHY-CytoCommunity outperforms existing hierarchical and non-hierarchical methods in identifying both coarse-grained tissue compartments and fine-grained cellular neighborhoods. Applied to a breast cancer cohort with clinical outcomes, the framework enables hierarchical prognostic stratification of patients and reveals survival-associated spatial patterns. HRCHY-CytoCommunity represents a general and scalable tool for deciphering tissue organization from single cells to multicellular modules, and ultimately to intact tissues and organs.