Extended Data Fig. 7: In-situ genomic analysis directly links level of genome rearrangement with histopathological phenotypes during PDAC progression.
From: Ordered and deterministic cancer genome evolution after p53 loss
a, Matched H&E and immunofluorescence for mKate/GFP in sequential sections after PDAC development in a KPCLOH mouse. White circles denote positions of SP and DP lesions with premalignant morphology and SP cells with PDAC morphology subjected to laser microdissection (LMD). b, Top panels - images of microdissected lesions noted in (a) - yellow lines denote boundaries of LMD. H&E as well as IF images are displayed. Bottom panels - corresponding genome wide copy number profiles of microdissected premalignant and malignant lesions. Red arrows denote distinguishing copy number alterations. c, Frequency plot of aggregate lesions collected by LMD and sequenced for each category. DP, n = 10; Pre SP, n = 9; SP-PDAC, n = 7. d, Matched GFP and Kate immunofluorescence and DNA FISH of chromosome 2, 9, and 10 in DP and SP cells within a focus of PDAC. Asterisks indicate cells with FISH signals consistent with polyploidy and loss of chromosome 9. e, Quantification of DNA-FISH foci in SP cells identified in KPCLOH mice before frank PDAC development (n = 5). For details of quantification, see Methods. f, DAPI based flow cytometric nuclear profiling of sorted Pre-SP cells capable of colony formation when plated at low density in-vitro (from Fig. 1j) (top-panel) and corresponding copy number profile with the sequencing imputed ploidy for the sample (bottom panel). MEF; Mouse Embryonic Fibroblasts. Scale bars a 1 mm, b 50 μm, d 10 μm. Gating strategy for f, see Supplementary Fig. 2.
