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Dependency-aware deep generative models for multitasking analysis of spatial omics data

Nature Methods volume 21, pages 1501–1513 (2024)Cite this article

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Abstract

Spatially resolved transcriptomics (SRT) technologies have significantly advanced biomedical research, but their data analysis remains challenging due to the discrete nature of the data and the high levels of noise, compounded by complex spatial dependencies. Here, we propose spaVAE, a dependency-aware, deep generative spatial variational autoencoder model that probabilistically characterizes count data while capturing spatial correlations. spaVAE introduces a hybrid embedding combining a Gaussian process prior with a Gaussian prior to explicitly capture spatial correlations among spots. It then optimizes the parameters of deep neural networks to approximate the distributions underlying the SRT data. With the approximated distributions, spaVAE can contribute to several analytical tasks that are essential for SRT data analysis, including dimensionality reduction, visualization, clustering, batch integration, denoising, differential expression, spatial interpolation, resolution enhancement and identification of spatially variable genes. Moreover, we have extended spaVAE to spaPeakVAE and spaMultiVAE to characterize spatial ATAC-seq (assay for transposase-accessible chromatin using sequencing) data and spatial multi-omics data, respectively.

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Fig. 1: The network architecture of dependency-aware deep generative models.
Fig. 2: Application of spaVAE to the LIBD human DLPFC data.
Fig. 3: Application of spaVAE to the mouse hippocampus Slide-seq V2 data.
Fig. 4: spaVAE for enhancing spatial resolution.
Fig. 5: Application of spaPeakVAE to the spatial ATAC-seq data.
Fig. 6: Application of spaMultiVAE to the spatial-CITE-seq data.

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Data availability

All data supporting the findings of the study are deposited and available at https://doi.org/10.6084/m9.figshare.21623148.v5 (ref. 68).

Code availability

An open-source software implementation of spaVAE, spaPeakVAE, spaMultiVAE, spaLDVAE and spaPeakLDVAE is available on GitHub: https://github.com/ttgump/spaVAE. It is also available in the Zenodo repository69.

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Acknowledgements

The study was supported by grant R15HG012087 (Z.W.) from the National Institutes of Health (NIH), grant BK20230781 (J.Z.) from the Natural Science Foundation of Jiangsu Province, and also funded in part by an Institutional Development Fund from The Children’s Hospital of Philadelphia (CHOP) and by CHOP’s Endowed Chair in Genomic Research. This work used the Extreme Science and Engineering Discovery Environment (XSEDE) through the allocation CIE170034, supported by the National Science Foundation grant number ACI1548562. The authors thank R. Cheng from the Tianjin University of Finance and Economics for assistance with the manuscript.

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Author notes

  1. These authors contributed equally: Tian Tian, Jie Zhang.

Authors and Affiliations

  1. School of Computer Science, National Engineering Research Center for Multimedia Software, Institute of Artificial Intelligence, and Hubei Key Laboratory of Multimedia and Network Communication Engineering, Wuhan University, Wuhan, Hubei, China

    Tian Tian

  2. Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Tian Tian & Hakon Hakonarson

  3. National Key Laboratory for Novel Software Technology, Nanjing University, Nanjing, Jiangsu, China

    Jie Zhang

  4. Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA

    Xiang Lin & Zhi Wei

  5. Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Hakon Hakonarson

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Contributions

T.T. conceived the project. T.T. and J.Z. designed the method. T.T., J.Z. and X.L. designed and conducted the experiments. Z.W. and H.H. supervised the study. T.T., J.Z., X.L., Z.W. and H.H. wrote the manuscript. All authors approved the manuscript.

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Correspondence to Zhi Wei.

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Nature Methods thanks Ofir Lindenbaum and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Primary Handling Editors: Hui Hua and Lin Tang, in collaboration with the Nature Methods team.

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Extended data

Extended Data Fig. 1 spaVAE for integrating batches of 10X mouse anterior and posterior brains data.

a, The spaVAE embedding of the mouse brain data with two regions (anterior and posterior) and two batches (section 1 and section 2), with colors and shapes denoting brain regions and batches. b, Clustering labels of the combined four samples, with colors denoting cluster labels. c, Alluvial plot of cluster proportions across different samples. d-e, Top genes identified (log fold change > 1 and Bayes factor > 10) by spaVAE within different clusters among the two sections of mouse anterior brain (d) and among the two sections of mouse posterior brain (e). Heatmaps display relative denoised averaged expression levels across the clusters.

Extended Data Fig. 2 Top spatially and nonspatially variable genes identified by spaLDVAE in the first 6 human DLPFC samples.

Top 4000 highly variable genes are used for this analysis.

Extended Data Fig. 3 Top spatially and nonspatially variable genes identified by spaLDVAE in the last 6 human DLPFC samples.

Top 4000 highly variable genes are used for this analysis.

Supplementary information

Supplementary Information

Supplementary Figs. 1–64, Tables 1 and 2, and Notes 1–14.

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Tian, T., Zhang, J., Lin, X. et al. Dependency-aware deep generative models for multitasking analysis of spatial omics data. Nat Methods 21, 1501–1513 (2024). https://doi.org/10.1038/s41592-024-02257-y

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