Additional file 2 of Patient-derived cell lines and orthotopic mouse model of peritoneal carcinomatosis recapitulate molecular and phenotypic features of human gastric adenocarcinoma
Creators: name: Song, Shumei
name: Xu, Yan
name: Huo, Longfei
name: Zhao, Shuangtao
name: Wang, Ruiping
name: Li, Yuan
name: Scott, Ailing W.
name: Pizzi, Melissa Pool
name: Wang, Ying
name: Fan, Yibo
name: Harada, Kazuto
name: Jin, Jiankang
name: Ma, Lang
name: Yao, Xiaodan
name: Shanbhag, Namita D.
name: Gan, Qiong
name: Roy-Chowdhuri, Sinchita
name: Badgwell, Brian D.
name: Wang, Zhenning
name: Wang, Linghua
name: Ajani, Jaffer A.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Additional file 2: Supplemental Fig. 1. Genetic alteration of three donor PC cells and cell lines. A. Whole-exome sequencing was performed in three donor PC cells IP-013 (GA0518), IP-107-02 (GA0804) and IP-116 (GA0825) directly from patients according to the Materials and Methods. Mutations in three donor PC cells were analyzed by a bioinformatician (S.Z.). B&amp;C. Karyotyping analyses of GA0518 (B) and Snu-1 (C) were performed by the Cytogenetics and Cell Authentication Core at MD Anderson as described in Materials and Methods. Abnormal chromosomal changes were observed in GA0518 (B) and Snu-1 (C). Red arrows indicate some of the chromosomal changes in each cell lines. Supplemental Fig. 2. Expression of CSC markers in the corresponding donor PC cell samples. Expression of several notable CSC markers (YAP1, EpCAM, ALDH1, and SOX9) in the corresponding donor PC cell samples (IP-013, IP-107-2, and IP-116) was determined by immunofluorescence staining as described in Materials and Methods. Supplemental Fig. 3. Expression of CD44, CD133, and EpCAM was evaluated by flow cytometry in the three new cell lines. Supplemental Fig. 4. Activation of stemness and oncogenic markers in three corresponding donor PC cells by CyTOF. CyTOF was performed in the donor PC cell samples IP-013, IP-107-2, and IP-116 according to the Materials and Methods. Activation of CSC markers (CD44 and ALDH1) and oncogenic pathways such as pS6, p-AKT, and mTOR was analyzed and identified by bioinformatician (R.W). Supplemental Fig. 5. Representative BLI images for GA0804 PDO model A. Representative BLI images from Day 1 to Day 36 in a GA0804 PDO mouse without PC metastasis; B. Representative BLI images in GA0804 PDO mouse with PC metastasis from Day 1 to Day 36. Supplemental Fig. 6. Representative BLI images for GA0825 and MKN45 PDO models. A. Representative BLI images from Day 1 to Day 27 in two PDO mouse models of GA0825 with no PC. B. Representative BLI images from Day 9 to Day 26 in two PDO mouse models of commercial GAC cell line MKN45 with no PC. Supplemental Fig. 7. IC50 of three new cell lines on chemo and target inhibitors. The cell line GA0518 (A), GA0804 (B), and GA0825 (C) were seeded onto 96-well plates with 3000 cells/well. After overnight incubation, cells were treated with the indicated doses of two chemo-5-FU and Docetaxel; and two target inhibitors- Erlotinib and RAD001 for 6 days and then CellTiter96 Aqueous one solution was added to each well (20ul to 100ul culture media) followed by 2 h incubation at 37 °C and absorbance reading at OD 490. GraphPad Prism7 was used for IC50 analysis by following the instruction from GraphPad.com ( https://www.graphpad.com/support/faq/how-to-determine-an-icsub50sub/ ).