Authors
Yuheng Zhu, Hao Zhang, Xianyu Zhang, Enshuang Zhao, Yinfei Dai, Hanbo Liu, Longyi Li, Xiyuan Mei, Yuxin Jin
Published in
Bioinformatics (Oxford, England). Aug 22, 2026. Epub Aug 22, 2026.
Abstract
Rice blast caused by Magnaporthe oryzae (M. oryzae) is a dynamic cross-kingdom infection process involving rapid transcriptional reprogramming and spatial tissue remodeling across successive stages. Although single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) provide complementary information, most integration methods analyze stages independently and ignore temporal continuity.
We developed the Plant Spatio-Temporal Integration Network (PSTN), which jointly learns stage-specific cell-to-space mappings through expression reconstruction and bidirectional maximum-similarity temporal regularization. Applied to matched rice scRNA-seq and ST data at 0, 12, and 24 h, PSTN outperformed Tangram, SpaGE, cell2location, and DestVI across three gene-set sizes. At 4,000 highly variable genes (HVGs), mean squared error (MSE) remained below 0.09 at all stages, with high gene-wise and spot-wise correlations. Mapping-structure and marker-based analyses recovered tissue-associated spatial and temporal patterns. Gene-permutation controls markedly reduced performance, demonstrating reliance on correct cross-modal gene correspondence. An independent mouse-cortex benchmark supported the static reconstruction component across systems. PSTN enables temporally coupled single-cell and spatial integration in dynamic host-pathogen systems.
PSTN is available at https://github.com/zhuyuheng111/PSTN. The Zenodo DOI for the repository is 10.5281/zenodo.21365720.
Supplementary data are available at Journal Name online.
PMID:
42633556
Bibliographic data and abstract were imported from PubMed on 23 Aug 2026.
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