Additional file 1 of Keratin 17 modulates the immune topography of pancreatic cancer
Creators: name: Delgado-Coka, Lyanne
name: Horowitz, Michael
name: Torrente-Goncalves, Mariana
name: Roa-Peña, Lucia
name: Leiton, Cindy V.
name: Hasan, Mahmudul
name: Babu, Sruthi
name: Fassler, Danielle
name: Oentoro, Jaymie
name: Bai, Ji-Dong K
name: Petricoin, Emanuel F.
name: Matrisian, Lynn M.
name: Blais, Edik Matthew
name: Marchenko, Natalia
name: Allard, Felicia D.
name: Jiang, Wei
name: Larson, Brent
name: Hendifar, Andrew
name: Chen, Chao
name: Abousamra, Shahira
name: Samaras, Dimitris
name: Kurc, Tahsin
name: Saltz, Joel
name: Escobar-Hoyos, Luisa F.
name: Shroyer, Kenneth R.
Publisher: name: figshare
Year: 2024
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Supplementary Material 1: Supplementary Fig. 1. Example of region of interest with manual dot annotation on the training set is illustrated. Expert pathologists manually placed dots on each cell over the ROIs a. Original mIHC ROI from PDAC testing case retrieved from QuIP; and ground truth (Superpixel Label and dot annotation) overlaid on original Image of b. K17 positive tumor cells (brown); c. K17 negative tumor cells (panCK in teal); d. CD163+ macrophages in green; e. CD16+ macrophages; f. CD8+ T cells in purple g. CD4+ T cells in red. Supplementary Fig. 2. Example of Region of interest with ground truth annotation. (A) Original mIHC ROI from PDAC testing case retrieved from QuIP (B) ground truth (Superpixel Label and dot annotation) overlaid on original Image. The following colors represent different stains: (black = CD4, purple = CD8, yellow = CD16, green = CD163, brown = K17+, Teal = K17. Supplementary Fig. 3. Immune cell density at different distances from the closest tumor nest margin. a. Bar graph depicting mean CD4+ cell density and standard deviation for 8 cases; b. CD8+ cell mean density; c. CD16+ and; d. CD163+ cells. Supplementary Fig. 4. High K17 expression is correlated with shorter survival in patients. Kaplan–Meier curves for the overall survival analysis of K17 from PDAC cases of all stages. P values were calculated using the log-rank test. HR, hazard ratio; K17, keratin 17; PDAC, pancreatic ductal adenocarcinoma. Supplementary Fig. 5. Flowchart of Multiplex Immunohistochemical Whole Slide Image Analysis Pipeline mIHC: multiplex immunohistochemistry, WSI: whole slide image, ROI: Region of Interest. Supplementary Fig. 6. There are more CD8+ T cells in K17-negative regions, regardless of histologic variant. Immune cell ratios in peritumoral and intratumoral K17-negative regions relative to K17-positive regions, ordered based on the density of immune cells in K17-positive zones. a–c. Peritumoral CD8+ T cell density ratios in conventional, foamy cell, and large duct PDAC variant cases. d–f. Intratumoral CD8+ T cell density ratios in conventional, foamy cell, and large duct PDAC variant cases. g–I. Representative H&amp;E photomicrographs of conventional, foamy cell, and large duct PDAC variants, respectively. Supplementary Table 1. List of targeted populations, antibodies, incubation times, chromogens, and localization of each marker used in mIHC staining. Supplementary Table 2. Model Validation. Supplementary Table 3. Mutational status.