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Robust decomposition of cell type mixtures in spatial transcriptomics

Nature Biotechnology volume 40, pages 517–526 (2022)Cite this article

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Abstract

A limitation of spatial transcriptomics technologies is that individual measurements may contain contributions from multiple cells, hindering the discovery of cell-type-specific spatial patterns of localization and expression. Here, we develop robust cell type decomposition (RCTD), a computational method that leverages cell type profiles learned from single-cell RNA-seq to decompose cell type mixtures while correcting for differences across sequencing technologies. We demonstrate the ability of RCTD to detect mixtures and identify cell types on simulated datasets. Furthermore, RCTD accurately reproduces known cell type and subtype localization patterns in Slide-seq and Visium datasets of the mouse brain. Finally, we show how RCTD’s recovery of cell type localization enables the discovery of genes within a cell type whose expression depends on spatial environment. Spatial mapping of cell types with RCTD enables the spatial components of cellular identity to be defined, uncovering new principles of cellular organization in biological tissue. RCTD is publicly available as an open-source R package at https://github.com/dmcable/RCTD.

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Fig. 1: Spatial transcriptomics data present challenges for cell type learning.
Fig. 2: RCTD enables cross-platform learning of cell types.
Fig. 3: RCTD performs cross-platform detection and decomposition of doublets.
Fig. 4: RCTD applied to cell type learning in Slide-seq datasets.
Fig. 5: RCTD maps cell types and subtypes in Slide-seq hippocampus data.
Fig. 6: RCTD enables the detection of cell-type-specific spatial patterns of gene expression.

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Data availability

Slide-seqV2 data generated for this study are available at the Broad Institute Single Cell Portal at https://singlecell.broadinstitute.org/single_cell/study/SCP948. Additional publicly available data from other studies that were used for analysis are also included in this repository.

Code availability

RCTD is implemented in the open-source R package RCTD, with source code freely available at https://github.com/dmcable/RCTD. Additional code used for analysis in this paper is available at https://github.com/dmcable/RCTD/tree/dev/AnalysisPaper.

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Acknowledgements

We thank R. Stickels for providing valuable input on the analysis. We thank members of the Chen lab, Irizarry lab and Macosko lab for helpful discussions. D.M.C. was supported by a Fannie and John Hertz Foundation Fellowship and an NSF Graduate Research Fellowship. This work was supported by an NIH Early Independence Award (1DP5OD024583 to F.C.), the Burroughs Wellcome Fund (F.C.) and the NHGRI (R01HG010647 to E.Z.M. and F.C.) as well as the Schmidt Fellows Program at the Broad Institute and the Stanley Center for Psychiatric Research. R.A.I. was supported by NIH grants R35GM131802 and R01HG005220.

Funding

Open Access funding enabled and organized by Projekt DEAL.

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Author notes

  1. These authors contributed equally: Fei Chen, Rafael A. Irizarry.

Authors and Affiliations

  1. Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA

    Dylan M. Cable

  2. Broad Institute of Harvard and MIT, Cambridge, MA, USA

    Dylan M. Cable, Evan Murray, Luli S. Zou, Aleksandrina Goeva, Evan Z. Macosko & Fei Chen

  3. Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA

    Dylan M. Cable, Luli S. Zou & Rafael A. Irizarry

  4. Department of Biostatistics, Harvard University, Boston, MA, USA

    Luli S. Zou & Rafael A. Irizarry

  5. Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA

    Evan Z. Macosko

  6. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA

    Fei Chen

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Contributions

D.M.C., F.C., R.A.I. and E.Z.M. conceived the study. F.C., E.M. and E.Z.M. designed the Slide-seq experiment. E.M. generated the Slide-seq data. D.M.C., R.A.I. and F.C. developed the statistical methods. D.M.C., F.C., R.A.I. and E.Z.M. designed the analysis. D.M.C., R.A.I., F.C., A.G. and L.S.Z. analyzed the data. D.M.C., F.C., R.A.I., E.Z.M. and L.S.Z. wrote the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Fei Chen or Rafael A. Irizarry.

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Supplementary Information

Supplementary Methods, Table 1 and Figs. 1–27.

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Cable, D.M., Murray, E., Zou, L.S. et al. Robust decomposition of cell type mixtures in spatial transcriptomics. Nat Biotechnol 40, 517–526 (2022). https://doi.org/10.1038/s41587-021-00830-w

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