Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors
Recent advancements in spatial transcriptomics technologies have significantly enhanced resolution and throughput, underscoring an urgent need for systematic benchmarking. Here, we generate serial tissue sections from colon adenocarcinoma, hepatocellular carcinoma, and ovarian cancer samples for systematic evaluation. Using these uniformly processed samples, we generate spatial transcriptomics data across four high-throughput platforms with subcellular resolution: Stereo-seq v1.3, Visium HD FFPE, CosMx 6K, and Xenium 5K. To establish ground truth datasets, we profile proteins on tissue sections adjacent to all platforms using CODEX and perform single-cell RNA sequencing on the same samples. Leveraging manual nuclear segmentation and detailed annotations, we systematically assess each platform's performance across capture sensitivity, specificity, diffusion control, cell segmentation, cell annotation, spatial clustering, and concordance with adjacent CODEX. The uniformly generated and processed multi-omics dataset could advance computational method development and biological discoveries. The dataset is accessible via SPATCH, a user-friendly web server for visualization and download.
Authors
- Ce Luo (ORCID: https://orcid.org/0000-0001-8024-6753)
- Yanping Zhao (ORCID: https://orcid.org/0000-0002-6806-1593)
- Zhidong Gao (ORCID: https://orcid.org/0000-0002-8415-7587)
- Zexian Zeng (ORCID: https://orcid.org/0000-0002-3905-3244)
- Zongxu Zhang (ORCID: https://orcid.org/0009-0006-2909-5842)
- Yufeng Li (ORCID: https://orcid.org/0000-0003-3906-8144)
- Peng Zhang (ORCID: https://orcid.org/0000-0001-9303-1639)
- Zhihua Liu (ORCID: https://orcid.org/0000-0003-4242-033X)
- Rui Zhang (ORCID: https://orcid.org/0000-0002-8132-6250)
- Zheng Zhang (ORCID: https://orcid.org/0000-0003-1470-6998)
- Yunfeng Wang (ORCID: https://orcid.org/0000-0002-8737-3103)
- Yufeng He (ORCID: https://orcid.org/0009-0000-3978-4103)
- Yahui Zhao
- Yuanguang Meng (ORCID: https://orcid.org/0000-0003-3813-8411)
- Pengfei Ren (ORCID: https://orcid.org/0000-0002-1085-6756)
- Haorui Zhang (ORCID: https://orcid.org/0000-0003-1517-1112)
- Xiaohong Li (ORCID: https://orcid.org/0000-0002-7084-1708)
- Xiuping Zhang (ORCID: https://orcid.org/0000-0002-8117-2925)
- Suyan Wang
Institutions
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Peking University (CN)
- Chinese PLA General Hospital (CN)
- Peking University People's Hospital (CN)
- Chengdu University (CN)
- Center for Life Sciences (CN)
- Tsinghua University (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-10-17
- DOI
- https://doi.org/10.1038/s41467-025-64292-3
- Citations
- 14
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 11.28
Funders
- National Natural Science Foundation of China
- Peking University
- National Science and Technology Major Project