Rm9103

Extracted tumours were fixed in 10% buffered formalin (Sigma) for 24-48 h at room temperature and then stored in 70% ethanol at 4°C. Samples were then paraffin-embedded, sectioned at 4 μm thickness and stained with haematoxylin and eosin (H&E). Ki67 (NB110-90592, Novus), TUNEL (homemade by the Pathology Research Program Laboratory), ER (ab80922, Abcam), PR (NCL-PR-312, Leica), HER2 (RM9103, Thermo Fisher Scientific), CK5 (NCL-LCK5, Leica), EGFR (28-0005, Invitrogen), p63 (VP-P960, Vector) and SMA (M0851, Dako) were used to further analyse tumour sections. All immunohistochemistry was performed as a service by the Pathology Research Program Laboratory (University Health Network, Toronto, Canada).

EDO grown in Matrigel were fixed in paraformaldehyde for 2 h and embedded in Histogel (Thermo Fisher Scientific, Waltham, MA). Adjacent fresh tumour tissues and Histogel embedded organoids were then fixed with 10% formalin for 24–48 h followed by fixation in 70% ethanol with containing eosin. Formalin-fixed paraffin embedded tumor tissues and organoids were cut into 4 μm thick slices and allowed to dry overnight at 60 °C. Prepared tissue sections were stained with appropriate antibodies using the BenchMark XT autostainer (Ventana Medical System, Tucson, AZ). Primary antibodies specific to p53 (Leica NCL-p53-D07, clone D07), CK7 (Dako M7018, clone OV-TL12130) and HER2 (Thermo Scientific RM9103, Rabbit monoclonal SP3) were used for IHC analysis. The slides were scanned and imaged using an Aperio Scanscope XT (Leica, Canada).