Spatial mapping of transcriptomic and lineage plasticity in metastatic pancreatic cancer [CosMx]

Patients with treatment-refractory pancreatic cancer often succumb to widespread systemic metastases; however, the transcriptomic heterogeneity that underlies recalcitrance to therapy remains understudied, particularly in the spatial context. We constructed high-resolution spatial maps of transcriptional heterogeneity, clonal architecture and lineage plasticity using spatially resolved transcriptomics (SRT) from 13 primary cancers and 36 corresponding liver, lung, and peritoneal metastases, collected via a rapid (“warm”) autopsy program. To validate findings from our SRT dataset at single-cell resolution, we performed CosMX SMI profiling (Nanostring) on 7 samples from 3 patients, including primary and/or liver metastasis. CosMx SMI profiling (Nanostring) was performed using a 1000-plex gene panel on fresh frozen tissues. A total of 90 Fields of View (FOVs, each 0.51 x 0.51 mm) from the tumour bed, juxtalesional region, and distant area were selected across seven tissue samples, guided by H&E-stained images obtained from a serial section. Four markers, DAPI, CD298/B2M, PanCK, and CD45, were used for cell segmentation.