Additional file 1 of Rational drug combination design in patient-derived avatars reveals effective inhibition of hepatocellular carcinoma with proteasome and CDK inhibitors
Creators: name: Lim, Jhin Jieh
name: Hooi, Lissa
name: Dan, Yock Young
name: Bonney, Glenn K.
name: Zhou, Lei
name: Chow, Pierce K.-H.
name: Chee, Cheng Ean
name: Toh, Tan Boon
name: Chow, Edward K.-H.
Publisher: name: figshare
Year: 2022
Subjects: Biochemistry
Space Science
Medicine
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer
Hematology
Virology

description: Additional file 1: Figure S1. Annexin V/PI assay in proteasome inhibitor-treated HCC PDXOs. (A and B) Flow cytometry analysis and corresponding quantification of annexin V/PI-stained PDXO1 (A) and PDXO11 (B) after 24-hour treatment with carfilzomib and ixazomib. Data presented as mean ± SD, n = 3. **, P &lt; 0.01; ***, P &lt; 0.001 compared to respective controls. Black and grey asterisks indicate comparison within early and late apoptosis groups, respectively. Statistical significance was determined using two-tailed Student’s t test. Figure S2. QPOP highlights Ixa+Dina as more effective than other ixazomib-based drug combinations. (A) Cluster heatmap of all two-drug combinations ranked based on QPOP output (viabilityTHLE2 – viabilityPDXO). Highest rank indicates maximal difference in viability and vice versa. The corresponding two-drug combinations are listed in Table S4. (B) Polygonograms depicting QPOP-derived two-drug interaction effects on PDXO viability between ixazomib (IXA), dinaciclib (DINA), sorafenib (SORA), regorafenib (REGO), oxaliplatin (OXA), and 5-fluorouracil (5FU) in HCC PDXOs. (C) Parabolic response surface maps showing the effects of ixazomib and dinaciclib on the therapeutic output (viabilityTHLE2 – viabilityPDXO) in HCC PDXOs. Figure S3. Annexin V/PI assay in HCC PDXOs treated with Ixa+Dina. (A and B) Analysis of Annexin V and PI-stained PDXO1 (A) and PDXO11 (B) after ixazomib and dinaciclib treatment for 24 hours. Figure S4. JNK pathway is involved in Ixa+Dina combined effects in HCC PDXOs. (A) Immunoblot analysis of the activation status of JNK, p38 and ERK in Ixa+Dina treated HCC PDXO1 and 11. (B) Relative mRNA levels of JUN and MAPK8 (JNK) after siRNA-mediated knockdown in Ixa+Dina treated PDXO1. Data presented as mean ± SD, n = 3. *, P &lt; 0.05; **, P &lt; 0.01. Statistical significance was determined using two-tailed Student’s t test. (C) Immunoblot analysis of JNK and c-Jun protein expression after siRNA transfection in Ixa+Dina treated PDXO1. (D) Immunoblots showing basal levels of JNK pathway proteins in panel of HCC PDXOs and THLE-2. Figure S5. Analysis of potential toxicities associated with ixazomib and dinaciclib drug treatment in vivo. (A and B) Representative H&amp;E images of the livers, kidneys, and spleens from drug-treated PDX1 (A) and PDX11 (B) tumor-bearing mice. Scale bar = 50 μm. Table S1. List of primary antibodies used. Table S2. List of drugs and corresponding drug identification ordered by rank as displayed in Fig. 2A. Table S3. QPOP drug combination design (OACD) consisting of 155 combinations for nine drugs at three dosage levels (− 1, 0, 1). The nine drugs include Ixazomib (Ixa), Dinaciclib (Dina), Carfilzomib (Car), Sorafenib (Sora), Lenvatinib (Len), Regorafenib (Rego), Cabozantinib (Cabo), Oxaliplatin (Oxa), and 5-Fluorouracil (5-FU). Table S4. Concentrations of drugs used for QPOP on HCC PDXOs and THLE-2 at the three dosage levels (− 1, 0, 1). Table S5. QPOP-derived two-drug combinations as shown in Fig. S2A. Values represent the concentrations (μM) used for each drug.