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Genome Med., Apr 01 2025, 17 (1) | https://doi.org/10.1186/s13073-025-01457-1
STopover captures spatial colocalization and interaction in the tumor microenvironment using topological analysis in spatial transcriptomics data
Sungwoo Bae1,2†, Hyekyoung Lee3†, Kwon Joong Na2,4, Dong Soo Lee5,6, Hongyoon Choi2,3,6* and Young Tae Kim4*
1Institute of Radiation Medicine, Medical Research Center, Seoul National University, Seoul, Republic of Korea
2Portrai, Inc., Seoul, Republic of Korea
3Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
4Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080 Republic of Korea
5Medical Science and Engineering, School of Convergence Science and Technology, POSTECH, Pohang, Republic of Korea
6Department of Nuclear Medicine, Seoul National University College of Medicine, Daehak-Ro, Jongno-Gu, 101 Seoul 03080, Republic of Korea
Sungwoo Bae and Hyekyoung Lee authors contributed equally to this work.
*Correspondence: Hongyoon Choi, Young Tae Kim
1Institute of Radiation Medicine, Medical Research Center, Seoul National University, Seoul, Republic of Korea
2Portrai, Inc., Seoul, Republic of Korea
3Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
4Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080 Republic of Korea
5Medical Science and Engineering, School of Convergence Science and Technology, POSTECH, Pohang, Republic of Korea
6Department of Nuclear Medicine, Seoul National University College of Medicine, Daehak-Ro, Jongno-Gu, 101 Seoul 03080, Republic of Korea
Sungwoo Bae and Hyekyoung Lee authors contributed equally to this work.
*Correspondence: Hongyoon Choi, Young Tae Kim
Abstract
Unraveling the spatial configuration of the tumor microenvironment (TME) is crucial for elucidating tumor-immune interactions based on immuno-oncology. We present STopover, a novel approach utilizing spatially resolved transcriptomics (SRT) data and topological analysis to investigate the TME. By gradually lowering the feature threshold, connected components (CCs) are extracted based on spatial distance and persistence, with Jaccard indices quantifying their spatial overlap, and transcriptomic profiles are permutated to assess statistical significance. Applied to lung and breast cancer SRT, STopover revealed immune and stromal cell infiltration patterns, predicted key cell-cell communication, and identified relevant regions, shedding light on cancer pathophysiology (URL: https://github.com/bsungwoo/STopover ).
논문정보
- Research article
- 2025년 04월 (BRIC 등록일 2025-04-24)
- 국내 연구진
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