CoCo-ST: Comparing and Contrasting Spatial Transcriptomics data sets using graph contrastive learning

TL;DR

CoCo-ST is a new method that improves the analysis of spatial transcriptomics data by highlighting subtle patterns that traditional methods might miss.

Contribution

CoCo-ST introduces a graph contrastive learning approach to better identify tissue-specific patterns by contrasting target and background datasets.

Findings

CoCo-ST enhances the detection of biologically relevant features in precancerous tissue.

The method effectively reduces the influence of dominant common patterns between datasets.

It was successfully demonstrated using serial mouse precancerous lung tissue samples.

Abstract

Traditional feature dimension reduction methods have been widely used to uncover biological patterns or structures within individual spatial transcriptomics data. However, these methods are designed to yield feature representations that emphasize patterns or structures with dominant high variance, such as the normal tissue spatial pattern in a precancer setting. Consequently, they may inadvertently overlook patterns of interest that are potentially masked by these high-variance structures. Herein we present our graph contrastive feature representation method called CoCo-ST (Comparing and Contrasting Spatial Transcriptomics) to overcome this limitation. By incorporating a background data set representing normal tissue, this approach enhances the identification of interesting patterns in a target data set representing precancerous tissue. Simultaneously, it mitigates the influence of dominant common patterns shared by the background and target data sets. This enables discerning biologically relevant features crucial for capturing tissue-specific patterns, a capability we showcased through the analysis of serial mouse precancerous lung tissue samples.

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