Spatial immune profiling complements genomic sequencing in biliary tract cancer: hypothesis-generating use cases.

Personalized therapy approaches targeting homologous recombination deficiency (HRD) in biliary tract cancer (BTC) remain poorly explored with limited clinical data available. Beyond BRCA1/2, the therapeutic implications of BRCA1-associated protein 1 (BAP1) alterations are unclear. We describe three patients with BTC and HRD-related mutations as hypothesis-generating use cases. We illustrate how integration of multiplexed imaging mass cytometry-based spatial immune profiling with genomic sequencing may help generate testable biological hypotheses beyond genomics alone. A patient with germline BRCA2-mutated BTC together with a positive HRD score was sensitive to platinum-based therapy and poly (ADP-ribose) polymerase inhibition. In contrast, a patient with loss of BAP1 was linked to a CD8+ T-cell enriched tumor microenvironment, classified as spatially immune enriched and responded long-term to subsequent immune checkpoint inhibition and tyrosine kinase inhibition therapy. These observations provide a rationale for integrated genomic and spatial immune profiling in BTC, which will require further prospective validation.