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Accurately Predicting Cell Type Abundance from Spatial Histology Image Through HPCell.

作者信息

Zhao Yongkang, Li Youyang, Yu Weijiang, Zhang Hongyu, Wang Zheng, Yang Yuedong, Zeng Yuansong

机构信息

School of Big Data and Software Engineering, Chongqing University, Chongqing, 400044, China.

College of Mathematics and Statistics, Chongqing University, Chongqing, 400044, China.

出版信息

Interdiscip Sci. 2025 Sep 3. doi: 10.1007/s12539-025-00757-9.


DOI:10.1007/s12539-025-00757-9
PMID:40903657
Abstract

Recent advancements in spatial transcriptomics (ST) have revolutionized our ability to simultaneously profile gene expression, spatial location, and tissue morphology, enabling the precise mapping of cell types and signaling pathways within their native tissue context. However, the high cost of sequencing remains a significant barrier to its widespread adoption. Although existing methods often leverage histopathological images to predict transcriptomic profiles and identify cellular heterogeneity, few approaches directly estimate cell-type abundance from these images. To address this gap, we propose HPCell, a deep learning framework for inferring cell-type abundance directly from H&E-stained histology images. HPCell comprises three key modules: a pathology foundation module, a hypergraph module, and a Transformer module. It begins by dividing whole-slide images (WSIs) into patches, which are processed by the pathology foundation module using a teacher-student framework to extract robust morphological features. These features are used to construct a hypergraph, where each patch (node) connects to its spatial neighbors to model complex many-to-many relationships. The Transformer module applies attention to the hypergraph features to capture long-range dependencies. Finally, features from all modules are integrated to estimate cell-type abundance. Extensive experiments show that HPCell consistently outperforms state-of-the-art methods across multiple spatial transcriptomics datasets, offering a scalable and cost-effective approach for investigating tissue structure and cellular interactions.

摘要

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本文引用的文献

[1]
Preeclampsia in mice carrying fetuses with APOL1 risk variants.

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[2]
Prescription psychostimulant use, admissions and treatment initiation and retention in pregnant people with opioid use disorder.

Nat Ment Health. 2024-7

[3]
MAPS: pathologist-level cell type annotation from tissue images through machine learning.

Nat Commun. 2024-1-2

[4]
Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology.

Nat Commun. 2023-12-13

[5]
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.

Nat Genet. 2023-1

[6]
Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.

Cell. 2022-5-12

[7]
Cell2location maps fine-grained cell types in spatial transcriptomics.

Nat Biotechnol. 2022-5

[8]
InterCellar enables interactive analysis and exploration of cell-cell communication in single-cell transcriptomic data.

Commun Biol. 2022-1-11

[9]
CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis.

BMC Bioinformatics. 2021-8-9

[10]
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.

Nat Biotechnol. 2021-3

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