Spatially Resolved Single-Cell Assessment of Pancreatic Cancer Expression Subtypes Reveals Co-expressor Phenotypes and Extensive Intratumoral Heterogeneity

Cancer Cancer
Genomics Genomics
Immunology Immunology
Technology Technology
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Peter Winter Peter Winter

Williams et al.▾ Williams, H.L., Costa, A.D., Zhang, J., Raghavan, S., Winter, P.S., Kapner, K.S., Ginebaugh, S.P., Vayrynen, S.A., Vayrynen, J.P., Yuan, C., Navia, A.W., Wang, J., Yang, A., Bosse, T.L., Kalekar, R.L., Lowder, K.E., Lau, M.C., Elganainy, D., Morales-Oyarvide, V., Rubinson, D.A., Singh, H., Perez, K., Cleary, J.M., Clancy, T.E., Wang, J., Mancias, J.D., Brais, L.K., Hill, E.R., Kozak, M.M., Linehan, D.C., Dunne, R.F., Chang, D.T., Koong, A.C., Hezel, A.F., Hahn, W.C., Shalek, A.K., Aguirre, A.J.#, Nowak, J.A., Wolpin, B.M.

Cancer Research , Volume 83

February, 2023


Pancreatic ductal adenocarcinoma (PDAC) has been classified into classical and basal-like transcriptional subtypes by bulk RNA measurements. However, recent work has uncovered greater complexity to transcriptional subtypes than was initially appreciated using bulk RNA expression profiling. To provide a deeper understanding of PDAC subtypes, we developed a multiplex immunofluorescence (mIF) pipeline that quantifies protein expression of six PDAC subtype markers (CLDN18.2, TFF1, GATA6, KRT17, KRT5, and S100A2) and permits spatially resolved, single-cell interrogation of pancreatic tumors from resection specimens and core needle biopsies. Both primary and metastatic tumors displayed striking intratumoral subtype heterogeneity that was associated with patient outcomes, existed at the scale of individual glands, and was significantly reduced in patient-derived organoid cultures. Tumor cells co-expressing classical and basal markers were present in > 90% of tumors, existed on a basal-classical polarization continuum, and were enriched in tumors containing a greater admixture of basal and classical cell populations. Cell-cell neighbor analyses within tumor glands further suggested that co-expressor cells may represent an intermediate state between expression subtype poles. The extensive intratumoral heterogeneity identified through this clinically applicable mIF pipeline may inform prognosis and treatment selection for patients with PDAC.