Deciphering spatial domains from spatial multi-omics with SpatialGlue

Deciphering spatial domains from spatial multi-omics with SpatialGlue

Nature Methods

10.1038/s41592-024-02316-4

https://doi.org/10.1038/s41592-024-02316-4

Yahui Long, Kok Siong Ang, Raman Sethi, Sha Liao, Yang Heng, Lynn van Olst, Shuchen Ye, Chengwei Zhong, Hang Xu, Di Zhang, Immanuel Kwok, Nazihah Husna, Min Jian, Lai Guan Ng, Ao Chen, Nicholas R. J. Gascoigne, David Gate, Rong Fan, Xun Xu, Jinmiao Chen

computational model

21 June 2024

Long, Y., Ang, K. S., Sethi, R., Liao, S., Heng, Y., van Olst, L., Ye, S., Zhong, C., Xu, H., Zhang, D., Kwok, I., Husna, N., Jian, M., Ng, L. G., Chen, A., Gascoigne, N. R. J., Gate, D., Fan, R., Xu, X., & Chen, J. (2024). Deciphering spatial domains from spatial multi-omics with SpatialGlue. Nature Methods, 21(9), 1658–1667. https://doi.org/10.1038/s41592-024-02316-4

Advances in spatial omics technologies now allow multiple types of data to be acquired from the same tissue slice. To realize the full potential of such data, we need spatially informed methods for data integration. Here, we introduce SpatialGlue, a graph neural network model with a dual-attention mechanism that deciphers spatial domains by intra-omics integration of spatial location and omics measurement followed by cross-omics integration. We demonstrated SpatialGlue on data acquired from different tissue types using different technologies, including spatial epigenome–transcriptome and transcriptome–proteome modalities. Compared to other methods, SpatialGlue captured more anatomical details and more accurately resolved spatial domains such as the cortex layers of the brain. Our method also identified cell types like spleen macrophage subsets located at three different zones that were not available in the original data annotations. SpatialGlue scales well with data size and can be used to integrate three modalities. Our spatial multi-omics analysis tool combines the information from complementary omics modalities to obtain a holistic view of cellular and tissue properties.

Attribution 4.0 International (CC BY 4.0)

This research / project is supported by the Agency for Science, Technology and Research - BMRC Central Research Fund (CRF, UIBR) Award
Grant Reference no. :

This research / project is supported by the Singapore Ministry of Health’s National Medical Research Council - Open Fund Individual Research Grant
Grant Reference no. : OFIRG18nov-0103

This research / project is supported by the National Research Foundation (NRF) - Competitive Research Programme
Grant Reference no. : NRF-CRP26-2021-0001

This research / project is supported by the Singapore Ministry of Health’s National Medical Research Council - Open Fund-Large Collaborative Grant
Grant Reference no. : MOH-OFLCG18May-0003

This research / project is supported by the Singapore National Medical Research Council - Open Fund-Large Collaborative Grant
Grant Reference no. : NMRC/OFLCG/003/2018

This research / project is supported by the Agency for Science, Technology and Research - AI, Analytics and Informatics (AI3) Horizontal Technology Programme Office (HTPO) seed grant
Grant Reference no. : C211118015

https://oar.a-star.edu.sg/communities-collections/articles/22191

1548-7091
1548-7105

Bioinformatics Institute