MSGPCA: Multi-Slice Graph PCA for replicate-aware Spatial Omics analysis

As spatial transcriptomics (ST) and spatial proteomics (SP) technologies mature, experimental designs are increasingly moving beyond single-slice analyses toward multi-slice studies involving one or more donors and experimental conditions. Although these designs enable the identification of reproducible spatial signals, they also introduce substantial biological heterogeneity, particularly when integrating non-serial slices or anatomically distinct regions. If not modeled carefully, such variation can blur slice-specific tissue structure, mask conserved molecular patterns, and limit the discovery of biologically relevant latent structure. Although dimension reduction is essential for representing high-dimensional molecular data in a lower-dimensional space, existing multi-slice methods typically enforce a globally shared representation that inadequately accommodates slice-level heterogeneity. To address this limitation, we propose Multi-Slice Graph Principal Component Analysis (MSGPCA), which decomposes molecular variation into shared spatial factors conserved across slices and slice-specific factors that capture local tissue microarchitecture. In downstream analyses, MSGPCA-derived representations recover spatial tissue structure, denoise molecular profiles, and reveal biologically interpretable metafeatures associated with shared and slice-specific biology. In a mass spectrometry imaging dataset comprising nonserial slices of ductal carcinoma in situ (DCIS) and invasive breast cancer (IBC), the shared factors captured broad biological differences across tissue regions, whereas the slice-specific factors revealed intratumoral spatial variation within the IBC microenvironment. In human dorsolateral prefrontal cortex ST data, MSGPCA recovered laminar cortical architecture across adjacent slices, closely aligning with expert pathologist annotations. Together, these findings demonstrate that MSGPCA resolves shared tissue architecture while preserving local microenvironmental variation in complex multi-slice spatial omics datasets.