MechanoMaST - a multimodal pipeline for spatially registering mechanical and transcriptomic tissue data

Abstract

Spatial-omics workflows enable spatially-resolved molecular analysis within tissues. Despite the prognostic value of tissue stiffness, these approaches have not yet incorporated direct, absolute mechanical measurements. This omission reflects several challenges, including sample requirements, low throughput, and the need for specialized equipment and complex data registration. Here, we introduce MechanoMaST (mechanics mapped to spatial transcriptomics), a workflow that combines absolute mechanical measurements with spatial-omics. It pairs atomic force microscopy-based nanoindentation stiffness maps with spatial transcriptomics maps from adjacent tissue cryosections. The two modalities are computationally co-registered to enable spatial correlation at 100 m resolution with a sub-10 m mean accuracy, providing ground-truth mechanical data directly linked to spatial gene expression. We demonstrate MechanoMaST in human colorectal cancer liver metastasis, generating a spatial resource from 10 patients and revealing a five-gene stiffness signature. MechanoMaST is readily adaptable to other tissues across development and disease, and extendable to additional spatial-omics modalities.