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2025

Luo Yuan/Zeng Zexian's team developed a spatial omics data analysis platform to empower disease mechanism research and drug development

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With the increasing maturity of traditional single-cell transcriptomics, spatial transcriptomics technology has rapidly emerged, allowing researchers to map the precise location and functional state of cells within tissue space for the first time [1-3]. More and more researchers are viewing spatial omics as a key tool for future disease mechanism research and targeted drug development [4-5]. However, with the accumulation of large amounts of data, the diversification of technical platforms and inconsistencies in standards have brought new challenges: How to integrate and standardize massive amounts of spatial omics data across platforms? How to systematically mine new biological insights and potential therapeutic targets from it?

On 〇〇, 2025, the Luo Yuan team from Northwestern University, in collaboration with Zeng Ze Xian from Peking University and collaborators, published a research paper in Science Advances: SOAR elucidates biological insights and empowers drug discovery through spatial transcriptomics. In this study, the authors developed SOAR (Spatial transcriptOmics Analysis Resource, https://soar.fsm.northwestern.edu/). SOAR is a database and platform that integrates spatial omics data integration and systematic analysis. By mining the changes in the spatial distribution and gene expression of cells in the tissue microenvironment under different disease states, SOAR can systematically identify key pathways, potential therapeutic targets and related drugs, thereby providing a data basis and analytical tools for disease mechanism analysis and drug development, and promoting precision medicine research.

SOAR is one of the most comprehensive spatial omics databases and analytical platforms known to date, integrating 3461 high-quality samples from 13 species, 42 tissue types, and 19 spatial transcriptomics technologies, and standardized processing through a unified workflow. SOAR not only focuses on data aggregation, but is also an open analytical platform, building standardized data processing workflows and rich data visualization and analysis tools.

In this study, the research team used the SOAR platform to focus on the analysis of cancer spatial omics data, and found that the polarization state of CXCL16⁺/SPP1⁺ macrophages reflects a key feature of the coordination of immune cell polarization in the tumor microenvironment. This finding not only enriches our understanding of tumor immune heterogeneity, but also provides a new perspective for future tumor immunotherapy target screening.

It is worth mentioning that SOAR has successfully integrated spatial omics data with drug target databases to provide users with target discovery and drug screening functions, thereby promoting future precision medicine research and drug development. In the study of ulcerative colitis, SOAR demonstrated its powerful ability in immune-related drug repositioning. Using the SOAR platform, the research team analyzed spatial omics data from healthy controls and ulcerative colitis patients treated with vedolizumab, and revealed the abnormal activation of the JAK-STAT pathway in T cells and myeloid cells (including macrophages and monocytes) in the lesion area. SOAR accurately identified the significant inhibitory effects of JAK inhibitors such as tofacitinib, TG-101348, and niclosamide in immune cells, which is particularly evident in vedolizumab-non-responders where traditional treatment is ineffective. SOAR's drug interference analysis showed that these small molecules can effectively inhibit the expression of various pro-inflammatory cytokines and their receptors (such as IL-2R, CSF1R, TNF, and IL23A), thereby downregulating inflammatory signaling pathways, reducing mucosal immune cell infiltration and epithelial damage. This result not only provides a treatment option with broad-spectrum immunomodulatory capabilities for patients with inflammatory bowel disease, but also provides data support for the design of future combination therapy clinical trials, highlighting the potential of SOAR in analyzing inflammatory mechanisms and promoting the development of immune-related drugs. In addition, by analyzing cancer spatial omics data, SOAR successfully predicted and verified sirolimus and trichostatin A as anti-cancer drug candidates that can target the PI3K/Akt/mTOR pathway to inhibit cancer cell growth and proliferation.

Yiming Li, Yanyi Ding, Saya Dennis, Meghan Hutch, and Jiaqi Zhou are the co-first authors of this paper. Yuan Luo and Ze Xian Zeng are the co-corresponding authors. The release of SOAR provides a solid foundation for future algorithm benchmarking, disease mechanism exploration, target discovery, and drug screening. With further technological advancements, SOAR is expected to become a daily tool for researchers and pharmaceutical developers, promoting the analysis of disease molecular mechanisms and the development of precision treatment strategies.

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