Fig. 4: Identification of tumor cells and stroma by PACpAInt-Cell type. | Nature Communications

Fig. 4: Identification of tumor cells and stroma by PACpAInt-Cell type.

From: Pacpaint: a histology-based deep learning model uncovers the extensive intratumor molecular heterogeneity of pancreatic adenocarcinoma

Fig. 4

a Workflow for cell type identification with PACpAInt-Cell type. PACpAInt-Neo is first applied to identify neoplastic regions, followed by PACpAInt-Cell type, which, inside these regions, distinguishes tumor cells from the stroma. PACpAInt-Cell type was trained on regions of 81 slides of the DISC cohort, annotated by two expert pathologists at the cell level. b Representative tiles identified as tumor or stroma by PACpAInt-Cell type in the TCGA validation cohort (112 μm square). c Performance of PACpAInt-Cell type to identify tumor and stroma cells in the BJN_U (top) and TCGA (bottom) validation cohorts, d correlation between the tumor cell/stroma ratio computed by PACpAInt-Cell type or with a computer-assisted calculation of the tumor stroma/ratio based on pan-cytokeratin immunohistochemistry (scale bar = 300 μm) (ratio stained area/total tumor area) (p value = 3.16e-09). p values were computed using a two-sided t-test, e Multivariate analyses of clinical/pathological factors and PACpAInt-cell type computed tumor/stroma ratio on disease-free (left, n = 428) and overall (right, n = 451) survival in the pooled DISC cohort and BJN_U + M validation cohorts. The circle represents the variable hazard ratio, while the whiskers represent the 95% confidence interval of that hazard ratio. P values for overall survival are: adjuvant treatment, p = 0.001935; PACpAInt-cell type, p = 0.020405, perineural invasion, p = 0.797476; differentiation, p = 0.731345; vascular invasion, p = 0.512674; Pathology N stage, p = 0.001960; PurIST-RNA, p = 0.001058; resection status, p = 0.002100; tumor size, p = 0.053910. P values for disease-free survival are: adjuvant treatment, p = 0.007799; PACpAInt-cell type, p = 0.008226, perineural invasion, p = 0.721716; differentiation, p = 0.779395; vascular invasion, p = 0.745392; pathology N stage, p = 0.000665; PurIST-RNA, p = 0.000153; resection status, p = 0.002868; tumor size, p = 0.019464.***p < 0.001; **p < 0.01; *p < 0.05; +p < 0.1; −p > 0.1. Source data are provided as a Source Data file.

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