Title
SPADE: An R package for spatial proximity analysis of differential expression
Authors
Mingke Wu*
Affiliation
Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191, China; *Corresponding author
Mingke Wu - E-mail: mingkewu@stu.pku.edu.cn
Article Type
Research Article
Date
Received July 1, 2026; Revised July 31,
2026; Accepted July 31, 2026, Published July 31, 2026
Abstract
Spatial transcriptomics enables characterization of tissue organization in situ, but accurate identification of spatially resolved transcriptional changes remains challenging because spot-level measurements are confounded by mixed-cell signals and contamination from neighboring cells. We developed SPADE, an R package integrated with Seurat, to identify contamination-aware differential expression between cells located near versus far from a reference cell type. Applying SPADE to 25 human NSCLC samples and validating findings in an independent cohort, we identified conserved distance-dependent transcriptional programs in tumor-proximal endothelial, stromal and immune cells, including pathways related to vascular homeostasis, extracellular matrix remodeling, antigen presentation and inflammatory signaling. Thus, data shows the spatially coordinated tumor microenvironment remodeling and demonstrate that accounting for spatial contamination improves the robustness of spatial transcriptomic inference. SPADE enables systematic discovery of spatial transcriptional reprogramming in complex tissues.
Keywords
Spatial transcriptomics, differential expression analysis, R package, cell-cell interaction, non-small cell lung cancer (NSCLC)
Citation
Wu Bioinformation 22(7): 3954-3962 (2026)
Edited by
P Kangueane
ISSN
0973-2063
Publisher
License
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
