Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution
Performing total RNA profiling on formalin-fixed, paraffin-embedded (FFPE) samples, the predominant sample conservation method in clinical practice, remains challenging for current spatial transcriptomics techniques. Here, we introduce Stereo-seq V2, which employs random primers to capture and sequence RNAs in situ on FFPE sections and provides single-cell resolution. The random-priming-based strategy offers unbiased transcript capturing and uniform gene body coverage, which increase the sensitivity to marker genes, the efficiency of non-polyadenylation (poly(A)) RNA profiling, and immune repertoire coverage. We demonstrated the robust performance of Stereo-seq V2 on clinical FFPE samples using triple-negative breast cancer (TNBC) sections and identified tumor-specific alternative splicing events. In a Mycobacterium tuberculosis (Mtb)-infected mouse model, we monitored gene expression dynamics of host and pathogen transcriptomes simultaneously by utilizing Stereo-seq V2. We also assembled immune repertoires and identified Mtb-specific BCR clones, which could also be observed in human tuberculous lung samples. These results highlight Stereo-seq V2's potential in biomedical research and personalized medicine.
Authors
- Zhifeng Deng (ORCID: https://orcid.org/0000-0003-3529-0549)
- Sha Liao (ORCID: https://orcid.org/0000-0001-5825-5514)
- Rong Xiang (ORCID: https://orcid.org/0000-0002-5521-3615)
- Gaoyang Wang (ORCID: https://orcid.org/0000-0001-6941-7363)
- Weihong Tan (ORCID: https://orcid.org/0000-0002-8066-1524)
- Longqi Liu (ORCID: https://orcid.org/0000-0002-5828-5542)
- Young Li
- Maoyuan Liu (ORCID: https://orcid.org/0000-0002-6875-535X)
- Zhaoxun Li (ORCID: https://orcid.org/0000-0003-1085-4053)
- Jialuo Li (ORCID: https://orcid.org/0000-0001-9760-4983)
- Jing Guo (ORCID: https://orcid.org/0000-0002-5654-3317)
- Xinxing Li (ORCID: https://orcid.org/0000-0003-3721-9447)
- Lei Han (ORCID: https://orcid.org/0000-0002-7535-7915)
- Xia Jiang (ORCID: https://orcid.org/0000-0003-0349-8126)
- Xuan Dong (ORCID: https://orcid.org/0000-0001-8288-322X)
- Tingting Cao (ORCID: https://orcid.org/0000-0002-2917-9513)
- Xiaoxi Zhou (ORCID: https://orcid.org/0009-0009-5368-6433)
- Qiaomei Yuan
- Yi Liu (ORCID: https://orcid.org/0000-0002-8801-9317)
- Jiajun Zhang (ORCID: https://orcid.org/0000-0003-2731-7158)
- Ao Chen (ORCID: https://orcid.org/0000-0002-9699-8340)
- Shanshan Li (ORCID: https://orcid.org/0000-0002-2064-2567)
- Dandan Li (ORCID: https://orcid.org/0000-0002-3527-3522)
- Chang Chen (ORCID: https://orcid.org/0000-0003-1008-1062)
- Xun Xu (ORCID: https://orcid.org/0000-0002-5338-5173)
- Yan Zhang (ORCID: https://orcid.org/0000-0002-6682-9917)
- Ying He (ORCID: https://orcid.org/0000-0003-0392-9686)
- Ming Xu (ORCID: https://orcid.org/0000-0003-2613-3824)
- Ying Qiu
- Xiaole Hu
- Jie Yuan (ORCID: https://orcid.org/0009-0006-7906-7612)
- Mei Yang (ORCID: https://orcid.org/0000-0003-1215-2688)
- Qiuling Chen (ORCID: https://orcid.org/0000-0003-0565-8082)
- Xin Huang (ORCID: https://orcid.org/0000-0002-6569-0095)
- Qin Wu (ORCID: https://orcid.org/0009-0004-3970-1389)
- Guifang Wu (ORCID: https://orcid.org/0009-0002-2169-6054)
- Xinya Zhang (ORCID: https://orcid.org/0009-0006-3138-9604)
- Fan Zhu (ORCID: https://orcid.org/0000-0002-2063-1630)
- Jie Zhai
- Huatang Deng (ORCID: https://orcid.org/0009-0009-1133-1124)
- Junqi Wu
- Xiawei Liu
- Haiying Liu
- Haiqiao Pan
- Tianbi Duan
- Zehao Wang
- Yu Zhao (ORCID: https://orcid.org/0000-0002-7482-3742)
Institutions
- BGI Group (China) (CN)
- Tongji University (CN)
- Shanxi Medical University (CN)
- Shanghai Jiao Tong University (CN)
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Renji Hospital (CN)
- Zhejiang Cancer Hospital (CN)
- Shanghai Pulmonary Hospital (CN)
- University of Chinese Academy of Sciences (CN)
- BGI Research (CN)
Publication Details
- Journal
- Cell
- Published
- 2025-08-28
- DOI
- https://doi.org/10.1016/j.cell.2025.08.008
- Citations
- 24
- Primary Topic
- RNA Research and Splicing
- Type
- article
- Field-Weighted Citation Impact
- 19.34
Funders
- National Natural Science Foundation of China
- National Key Research and Development Program of China
- Chinese Academy of Medical Sciences Initiative for Innovative Medicine
- Science and Technology Department of Zhejiang Province