eMCI: An Explainable Multimodal Correlation Integration Model for Unveiling Spatial Transcriptomics and Intercellular Signaling

Abstract

Current integration methods for single-cell RNA sequencing (scRNA-seq) data and spatial transcriptomics (ST) data are typically designed for specific tasks, such as deconvolution of cell types or spatial distribution prediction of RNA transcripts. These methods usually only offer a partial analysis of ST data, neglecting the complex relationship between spatial expression patterns underlying cell-type specificity and intercellular cross-talk. Here, we present eMCI, an explainable multimodal correlation integration model based on deep neural network framework. eMCI leverages the fusion of scRNA-seq and ST data using different spot–cell correlations to integrate multiple synthetic analysis tasks of ST data at cellular level. First, eMCI can achieve better or comparable accuracy in cell-type classification and deconvolution according to wide evaluations and comparisons with state-of-the-art methods on both simulated and real ST datasets. Second, eMCI can identify key components across spatial domains responsible for different cell types and elucidate the spatial expression patterns underlying cell-type specificity and intercellular communication, by employing an attribution algorithm to dissect the visual input. Especially, eMCI has been applied to 3 cross-species datasets, including zebrafish melanomas, soybean nodule maturation, and human embryonic lung, which accurately and efficiently estimate per-spot cell composition and infer proximal and distal cellular interactions within the spatial and temporal context. In summary, eMCI serves as an integrative analytical framework to better resolve the spatial transcriptome based on existing single-cell datasets and elucidate proximal and distal intercellular signal transduction mechanisms over spatial domains without requirement of biological prior reference. This approach is expected to facilitate the discovery of spatial expression patterns of potential biomolecules with cell type and cell–cell communication specificity.