Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

Recent advances in spatial transcriptomics (ST) enable gene expression measurements from a tissue sample while retaining its spatial context. This technology enables unprecedented in situ resolution of the regulatory pathways that underlie the heterogeneity in the tumor and its microenvironment (TME). The direct characterization of cellular co-localization with spatial technologies facilities quantification of the molecular changes resulting from direct cell-cell interaction, as occurs in tumor-immune interactions. We present SpaceMarkers, a novel bioinformatics algorithm to infer molecular changes from cell-cell interaction from latent space analysis of ST data. We apply this approach to infer molecular changes from tumor-immune interactions in Visium spatial transcriptomics data of metastasis, invasive and precursor lesions, and immunotherapy treatment. Further transfer learning in matched scRNA-seq data enabled further quantification of the specific cell types in which SpaceMarkers are enriched. Altogether, SpaceMarkers can identify the location and context-specific molecular interactions within the TME from ST data. The HCC sample was obtained from a Phase I clinical trial that examined cabozantinib plus nivolumab as neoadjuvant therapy for advanced hepatocellular carcinoma. The PDAClymphnode was collected from a patient with pancreatic adenomarcinoma that received noeadjuvant therapy with a pancreatic cancer vaccine (GVAX). The PanIN was collected from a treatment naive pancreatic cancer patient. All three samples were analyzed using spatial transcriptomics. None of the samples had experimental replicates. We performed latent space factorization of the 10x Visium spatial transcriptomics and used SpaceMarkers to identify genes associated with spatially overlapping latent features representing different cell types. For the HCCsinglecell sample, the tumor was enzymatically dissociated into single cells upon surgical resection. Tumor was minced and dissociated in digestion medium containing 0.1% (w/v) collagenase type IV (Invitrogen) in PBS at 37°C for 30 minutes on a shaking incubator set at 60 rpm. Cell collection was enriched with Percoll 40%−80% (GE Life Sciences) at 2000 × g for 25 minutes at RT without break, eliminating debris and erythrocytes. *** Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns ***