To calculate each cell population, and for visual display (Supplementary Table 3), each cell was classified to one of 18 groups: CK+, CD45+, FAP+, aSMA+, Thy1+, FSP-1+, aSMA+/FAP+, FAP+/Thy1+, FAP+/FSP-1+, aSMA+/Thy1+, aSMA+/FSP-1+, FSP-1+/Thy1+, aSMA+/FAP+/Thy1+, aSMA+/FAP+/FSP-1+, FAP+/FSP-1+/Thy1+, aSMA+/FSP-1+/Thy1+, aSMA+/FAP+/FSP-1+/Thy1+, or “other”. Pericytes are known to express alpha-SMA (39 (link)). To avoid misinterpretation, based on histology, we deselected the areas of blood vessels in the stroma and the selected ROIs were composed only of tumor, tumor stroma interface and stroma (excluding the blood vessels), so that pericytes are not included in the final data. We then generated 19 possible marker expression patterns based on the expression of α-SMA, Thy-1, FAP+, and FSP-1. In our cohort we had equal numbers of two different subsets of ILC (classic ILC vs Pleomorphic ILC). Patterns of distribution according the nearest neighbor distance were calculated for each CAF phenotype to tumor cells using the X and Y coordinates of each cell with Phenoptr script from R studio (Akoya Biosciences). We then compared the proximities of each CAF subtype to the tumor cells between the two histological subtypes of ILC using IBM SPSS statistics software 24.
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