Additional file 2 of Implementing patient derived organoids in functional precision medicine for patients with advanced colorectal cancer
Creators: name: Cartry, Jérôme
name: Bedja, Sabrina
name: Boilève, Alice
name: Mathieu, Jacques R. R.
name: Gontran, Emilie
name: Annereau, Maxime
name: Job, Bastien
name: Mouawia, Ali
name: Mathias, Pierre
name: De Baère, Thierry
name: Italiano, Antoine
name: Besse, Benjamin
name: Sourrouille, Isabelle
name: Gelli, Maximiliano
name: Bani, Mohamed-Amine
name: Dartigues, Peggy
name: Hollebecque, Antoine
name: Smolenschi, Cristina
name: Ducreux, Michel
name: Malka, David
name: Jaulin, Fanny
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Pharmacology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy
subject: Mental Health
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 2: Supplementary Fig. 1. (A) Test of 3 tumor digestion protocols based on the evaluation of viable cell number and cell viability signal. (B) CK20 and CDX2 staining. Scale Bar, 300 μm. (C) Bar graph of the total number of COSMIC referenced mutations per PDO. Data are presented as the mean + SD in A (n = 3). Significance is determined with one‐way ANOVA with Tukey’s multiple comparisons test in A. Supplementary Fig. 2. (A) Graph presenting PDO area as a function of relative ATP signal for 3 different PDOs: CGR002, CGR0029, CGR0039. Each dot is the average area of &gt; 50 PDOs and the relative ATP signal of the entire well. 8 dots are displayed, representing 8 different conditions: 2 drugs (5FU and Oxaliplatin) at three different concentrations and one control condition per drug. (B) Graph A is annotated with 3 representative images of CGR0002 single PDO outlined with a pink line delimiting the segmentation zone for area extraction. (C) Graph presenting PDO area as a function of relative ATP signal for CGR0002 tested with 25 drugs at 3 concentrations in triplicate. Each dot is one well. (D) Graph presenting relative LDH signal as a function of relative ATP signal for CGR0002 tested for 6 drugs (5FU, Azacitidine, Bortezomib, Carboplatin, Cobimetinib and Docetaxel) at 3 concentrations in triplicate. Each dot is one well. Correlation is determined with the Pearson correlation coefficient (R) in A, C and D. Supplementary Fig. 3. (A) Drug test technical reproducibility for the other replicate combinations (supplementary data of Fig. 3E) assessed by the viability percentage obtained over one experimental run. (B) Bar graphs of the response of CGR0002, CGR0029 and CGR0039 to 5FU and Oxaliplatin before and after the freezing/thawing process. (C) Drug test biological reproducibility (supplementary data of Fig. 3F). Data are presented as the mean of triplicates in A (CGR0025 screened four times on the same run with 4 drugs at 3 concentrations (12 dots)), as the mean + SD of technical triplicates in B, as the mean of triplicates in C (CGR0002 screened on two different runs with a 2-week interval for 25 drugs at 3 concentrations (75 dots). Correlation is determined with the Pearson correlation coefficient (R). Supplementary Fig. 4. Sensitivity of the 25 PDOs to 24 drugs at 3 concentrations (supplementary data of Fig. 3G, 1 color line/PDO). Data are presented on the right panels as the mean response ± SD of the 25 PDOs to each drug. Supplementary Fig. 5. (A) Scatterplot of the PDO scores to 4 different couples of drugs (supplementary data of Fig. 4B). Each dot represents the score of one PDO. (B) Heatmap of scores for all 25 drugs against the 25 PDOs. Drugs were clustered according to their belonging to the CRC therapeutic arsenal (CRC SOC). Correlation is determined with the Pearson correlation coefficient (R) in A.