G 415

The human GBC cell line NOZ was obtained from the Health Science Research Resources Bank (Osaka, Japan; No. JCRB1033). The other three GBC cell lines, G-415, TGBC-1TKB (TGBC1), and TGBC-2TKB (TGBC2), were purchased from RIKEN BioResource Center (Ibaraki, Japan; No. RCB2640, RCB1129, and RCB1130). NOZ, TGBC1, and TGBC2 were grown in Dulbecco’s Modified Eagle Medium (DMEM high glucose; Corning, NY, USA) supplemented with 5% fetal bovine serum (FBS, Thermo Fisher Scientific Inc., Waltham, MA, USA) and 10 units/mL penicillin and 10 mg/mL streptomycin (1% P/S, Thermo Fisher Scientific). The G-415 cells were grown in RPMI 1640 medium (Thermo Fisher Scientific) supplemented with 10% FBS and 1% P/S. Cells were maintained at 37 °C in a humidified atmosphere containing 5% CO₂. All cell lines were routinely tested for mycoplasma by PCR and authenticated by short tandem repeat DNA profiling.

Cancer cell lines: G-415 (gallbladder cancer) (Riken BioResource Center, Ibaraki, Japan), EIH1299 (non-small cell lung cancer) expressing p53 R273H in a ponasterone A inducible manner (kindly provided by Karen Vousden, Francis Crick Institute, London, UK) [43 (link)] and Panc-1 (pancreatic ductal adenocarcinoma) (ATCC, Manassas, VA, USA) were grown on DMEM F-12 supplemented with 10% heat-inactivated fetal bovine serum (HyClone, Logan, UT, USA), 100 units/mL penicillin and 100 μg/mL streptomycin at 37 °C in a humidified atmosphere containing 5%-CO₂.

Six gallbladder cancer cell lines were used for this study. TGBC2TKB, TGBC24TKB, and G-415 were purchased from RIKEN Bio Resource Center, Ibaraki, Japan. OCUG-1 and NOZ were obtained from Health Science Research Resources Bank, Osaka, Japan. SNU-308 was obtained from Korean Cell Line Bank, Seoul, Korea. TGBC2TKB, SNU-308, TGBC24TKB, G-415, OCUG-1 were cultured in DMEM high glucose, 10% FBS, 1% penicillin/streptomycin. For NOZ DMEM high glucose and DMEM low glucose was used in 1:1 ratio along with 10% FBS, 1% penicillin/streptomycin. Cell lines were maintained in humidified incubator with 5% CO₂ at 37°C.

The human GBC cells G-415 and TGBC2KB were obtained from Riken BioResource Center (Ibaraki, Japan). G-415 were grown in Roswell Park Memorial Institute (RPMI) 1640 medium and TGBC-2TKB were grown in Dulbecco's Modified Eagle's Medium (high glucose), supplemented with 10% fetal bovine serum, 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin and maintained in a 37°C atmosphere containing 5% CO₂.

The GBC cell lines, OCUG-1 and NOZ were obtained from Health Science Research Resources Bank, Osaka, Japan. TGBC2TKB, TGBC24TKB and G-415 were purchased from RIKEN Bio Resource Center, Ibaraki, Japan. SNU-308 was obtained from Korean Cell Line Bank, Seoul, Korea. GB-d1 was authenticated by short tandem repeat analysis. The properties and culture conditions of the GBC cell lines, TGBC2TKB, SNU-308, G-415, TGBC24TKB, NOZ, OCUG-1 and GB-d1 are provided in Additional file 1. All cell lines were maintained in humidified incubator with 5 % CO₂ at 37 °C.

In this study, we analyzed 167 human primary GBC samples as well as 39 non-GBC samples and the corresponding matched normal tissue in most cases using exome-seq, and/or low-pass whole-genome sequencing and/or RNA-seq (Supplementary Table 1). Fresh frozen samples used in the study were obtained from patients undergoing extirpative surgery for GBC. This study was conducted with IRB approval (Pontificia Universidad Católica de Chile IRB, Institutional Human Ethics Committee of Jiwaji University (India) and Seoul National University Hospital IRB (Seoul)) and written patient informed consent. Human tissue samples were de-identified prior to their shipment and analysis and are not considered human subject research under the US Department of Human and Health Services regulations and related guidance (45 CFR Part 46). Basic demographic information for the patient samples in the study, where available, is included in Supplementary Data 1. Tissue processing as well as simultaneous extraction of high-quality genomic DNA and total RNA from the same samples were performed as previously described^{47 (link)}. The study also included GBC cell lines TGBC24TKB, TGBC2TKB, G-415 (RIKEN Bio Resource Center, Ibaraki, Japan), OCUG-1 (Health Science Research Resources Bank, Osaka, Japan), SNU-308 (Korean Cell Line Bank, Seoul, Korea), GB-d1 (From Dr. Masao Tanaka’s lab, Japan)^{48 (link)}.