Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures

Shunxing Bao; Sichen Zhu; Vasantha L Kolachala; Lucas W. Remedios; Yeonjoo Hwang; Yutong Sun; Ruining Deng; Can Cui; Yike Li; Jia Li; Joseph T. Roland; Qi Liu; Ken S. Lau; Subra Kugathasan; Peng Qiu; Keith T. Wilson; Lori A. Coburn; Bennett A. Landman; Yuankai Huo

arXiv · 2308.10166

Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures

Shunxing Bao·Sichen Zhu·Vasantha L Kolachala·Lucas W. Remedios·Yeonjoo Hwang·Yutong Sun·Ruining Deng·Can Cui·Yike Li·Jia Li·Joseph T. Roland·Qi Liu·Ken S. Lau·Subra Kugathasan·Peng Qiu·Keith T. Wilson·Lori A. Coburn·Bennett A. Landman·Yuankai Huo

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Abstract

Crohn's disease (CD) is a chronic and relapsing inflammatory condition that affects segments of the gastrointestinal tract. CD activity is determined by histological findings, particularly the density of neutrophils observed on Hematoxylin and Eosin stains (H&E) imaging. However, understanding the broader morphometry and local cell arrangement beyond cell counting and tissue morphology remains challenging. To address this, we characterize six distinct cell types from H&E images and develop a novel approach for the local spatial signature of each cell. Specifically, we create a 10-cell neighborhood matrix, representing neighboring cell arrangements for each individual cell. Utilizing t-SNE for non-linear spatial projection in scatter-plot and Kernel Density Estimation contour-plot formats, our study examines patterns of differences in the cellular environment associated with the odds ratio of spatial patterns between active CD and control groups. This analysis is based on data collected at the two research institutes. The findings reveal heterogeneous nearest-neighbor patterns, signifying distinct tendencies of cell clustering, with a particular focus on the rectum region. These variations underscore the impact of data heterogeneity on cell spatial arrangements in CD patients. Moreover, the spatial distribution disparities between the two research sites highlight the significance of collaborative efforts among healthcare organizations. All research analysis pipeline tools are available at https://github.com/MASILab/cellNN.

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Shunxing Bao, Sichen Zhu, Vasantha L Kolachala, Lucas W. Remedios, Yeonjoo Hwang, Yutong Sun, Ruining Deng, Can Cui, Yike Li, Jia Li, Joseph T. Roland, Qi Liu, Ken S. Lau, Subra Kugathasan, Peng Qiu, Keith T. Wilson, Lori A. Coburn, Bennett A. Landman, Yuankai Huo. 2023-08-20. Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures. https://arxiv.org/abs/2308.10166

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