Spatial transcriptomics & Cell-to-cell communication

• Spatial transcriptomics

• Probes on slide

• PDAC

• CNV inference from scRNAseq to identify tumor cells

• H&E staining

• Integration of spatial and scRNAseq with MIA (hypergeometric test)

• Parameter sweep

• MIA maps of PDAC

• Infammatory fibroblast signal in cancer regions

• Sub-clustering / sub-regioning

• Stress response predicted to derive from fibroblasts in cancer regions

• Spots encompass dozens of cells

• Cell-to-cell communication

• Types of cell signaling events

• Downstream consequences of signaling

• Goal of Cell-to-cell interaction analysis:

  • What cells are interacting?

  • How are they interacting?

  • What are the consequences of the interactions?

• CCC in kidney development

• Kumar et al Cell Reports 2018

  • ID interactions that correlate with tumor growth

• SingleCellSignalR (Cabello-Aguilar et al 2020)

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