For digital pathology, we utilized the Visiopharm image analysis software version 2018.9.5.5952 (Visiopharm A/S, Hørsholm, Denmark). The Tissue Array module was used to identify and extract individual cores on the TMAs and the Tissue Align module to align the pan-cytokeratin stained image with its corresponding fluorescence image (Supplementary Fig. 7a, step 1). Image analysis protocol packages (APPs) developed by our group41 were used to automatically: (1) Define parenchymal and stromal regions as pan-cytokeratin positive and negative, respectively (Supplementary Fig. 7a, step 2). Calculate the proportion of immune cell subsets based on co-localization of selected markers (Supplementary Fig. 7a, step 3). Calculate the proportion of PD-L positive cells. In addition, we designed an APP using the Tissue Author module, in order to calculate the proportion of GATA3, CK5/6 or double-positive positive cells. For GATA3 and CK5/CK6 detection, tumors were classified as positive if more than 50% of the carcinoma cells expressed the marker. For all markers, we selected a threshold visually to differentiate between positive and unspecific staining. The threshold was verified by an experienced pathologist. We applied the following scoring algorithm to calculate cell fractions (here shown for T helper cells):

The proportion of infiltrating immune cells was consistent across the 3 tissue cores from the same tumor; average Pearson correlation coefficient: 0.67 (panel 1) and 0.77 (panel 2).

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