Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing

Xiaofeng Wu; Weize Xu; Lulu Deng; Yue Li; Zhongchao Wang; Leqiang Sun; Anran Gao; Haoqi Wang; Xiaodan Yang; Chengchao Wu; Yanyan Zou; Keji Yan; Zhixiang Liu; Lingkai Zhang; Guohua Du; Liyao Yang; Da Lin; Junqiu Yue; Ping Wang; Yunyun Han; Zhenfang Fu; Jinxia Dai; Gang Cao

doi:10.1038/s41551-024-01205-7

Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing

Nat Biomed Eng. 2024 May 14. doi: 10.1038/s41551-024-01205-7. Online ahead of print.

Authors

Xiaofeng Wu^#^{1

2}, Weize Xu^#^{1

2}, Lulu Deng^{1

2}, Yue Li^{1

2}, Zhongchao Wang^{1

2}, Leqiang Sun^{1

2}, Anran Gao^{1

2}, Haoqi Wang^{1

2}, Xiaodan Yang³, Chengchao Wu^{1

2}, Yanyan Zou^{1

2}, Keji Yan^{1

2}, Zhixiang Liu^{1

2}, Lingkai Zhang^{1

2}, Guohua Du^{1

2}, Liyao Yang^{1

2}, Da Lin^{1

2}, Junqiu Yue⁴, Ping Wang^{5

6}, Yunyun Han³, Zhenfang Fu⁷, Jinxia Dai^{8

9}, Gang Cao^{10

11

12

13}

Affiliations

¹ State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
² College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
³ School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
⁴ Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
⁵ Britton Chance Centre for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China.
⁶ MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Centre for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China.
⁷ Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
⁸ State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China. jxdai@mail.hzau.edu.cn.
⁹ College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. jxdai@mail.hzau.edu.cn.
¹⁰ State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China. gcao@mail.hzau.edu.cn.
¹¹ College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. gcao@mail.hzau.edu.cn.
¹² Faculty of Life and Health Sciences, and Shenzhen-Hong Kong Institute of Brain Science and The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China. gcao@mail.hzau.edu.cn.
¹³ NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China. gcao@mail.hzau.edu.cn.

^# Contributed equally.

PMID: 38745110
DOI: 10.1038/s41551-024-01205-7

Abstract

Technology for spatial multi-omics aids the discovery of new insights into cellular functions and disease mechanisms. Here we report the development and applicability of multi-omics in situ pairwise sequencing (MiP-seq), a method for the simultaneous detection of DNAs, RNAs, proteins and biomolecules at subcellular resolution. Compared with other in situ sequencing methods, MiP-seq enhances decoding capacity and reduces sequencing and imaging costs while maintaining the efficacy of detection of gene mutations, allele-specific expression and RNA modifications. MiP-seq can be integrated with in vivo calcium imaging and Raman imaging, which enabled us to generate a spatial multi-omics atlas of mouse brain tissues and to correlate gene expression with neuronal activity and cellular biochemical fingerprints. We also report a sequential dilution strategy for resolving optically crowded signals during in situ sequencing. High-throughput in situ pairwise sequencing may facilitate the multidimensional analysis of molecular and functional maps of tissues.

Abstract

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