Spatial reconstruction of single-cell gene expression data

· by Shengtong Han · Read in about 3 min · (517 words) ·


  • infer spatial locations of various cell types which will determine the cell fate and behavior

  • RNA staining only assays a small number of transcripts and RNA-seq can measure the global gene expression, but separates the cells from their native spatial context.

  • they develop Seurat to localize the cells by integrating single cell RNA-seq data and in situ RNA patterns.



Figure 1 gives the overview of the method.

  1. collect single cell RNA-seq data from dissociated cells while, spatial original context information is lost

  2. in situ hybridization patterns for a series of landmark genes (Landmark genes were selected as those widely expressed across lineage and were found to have good predictive power for inferring the expression of other genes that are not directly measured in the assay.)

  3. use machine learning to infer expression pattern (64 bins)

  4. build expression model of 47 landmark genes in each region of interest

  5. infer cell’s spatial origin probabilistically by comparing each cell’s expression of landmark genes to expression model of each region.

Seurat has the following features

  • due to the sparsity of single cell RNA seq data, use co-expression patterns across cells to impute the expression of each landmark gene in each cell

  • relates the continuous imputed RNA-seq expression levels of each landmark gene to the binary spatial expression values using a mixture model

  • constructs a multivariate normal model for the joint expression of the landmark genes based on these mixture models

  • infers the spatial origin of each profiled cell by calculating a posterior probability for each cell-bin pair, allowing determination of the cell’s likely position(s) and confidence in the mapping

Matching binary in situ hybridizations to continuous, noisy RNA-seq data

  • Single cell RNA-seq data are confounded with technical noise. Seurat leverages the fact that RNA-seq measures multiple genes that are co-regulated with the landmark genes and uses these genes to impute the values of the landmark genes

  • for each landmark gene, Seurat relate its continuous imputed RNA-seq expression levels to its binary state in the landmark map. Seurat relates the typical bimodal distribution of its imputed expression measurements to the on and off modes of the spatial reference map. Fit the distribution of imputed values of each landmark gene as a mixture of two Gaussian distributions by using R function normalmixEM with two modifications.

Probabilistic inference of spatial origin

  • Seurat constructs a model for the joint expression of the landmark genes in each bin based on the parameters of the mixture models and the binary spatial reference map, i.e., build 64 distinct multivariate normal models.

  • Seurat calculates the likelihood that this cell’s expression of the landmark gene reflects the on state, and thus, a probability that this cell originated from each of 64 bins marked as on in the reference map

  • Seurat infers the posterior probability that a cell is originated from each of bins in the reference map

Possible improvements

  • use continuous gene expression not just “on” and “off” in reference map

  • what other information could be utilized to guide the cell assignments

  • is it biologically feasible to use a barcode to label the spatial origins for each cell?