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

Spatial-omics workflows enable molecular analysis within tissue spatial context. Despite the prognostic value of tissue stiffness, these approaches have not incorporated direct, absolute mechanical measurements. This omission reflects several challenges, including sample requirements, low throughput, specialized equipment, and complex data registration.

Here, we introduce MechanoMaST (mechanics mapped to spatial transcriptomics), the first workflow to combine 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 direct spatial correlation at 100 µm resolution, with mapping accuracy quantified through error propagation, 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 four-gene stiffness signature. MechanoMaST is readily adaptable to other tissues across development and disease, and extendable to additional spatial-omics modalities in adjacent sections.