Cell lines and culture condition
Human MM cell lines (RPMI8226, U266, KMS-11, H929, OPM-2, MM1.S, ADR-R/RPMI8226, KMS-11/BTZ, OPM-2/BTZ, H929 CRBN sh#395, H929 CRBN sh#610, OPM-2 CRBN sh#395, OPM-2 CRBN sh#610, OPM-2 CRBN KO, and Dex-R/MM1.S) were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. KHYG-1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin in the presence of 2–20 ng/mL IL-2. Cell lines were acquired as follows: RPMI8226, U266, H929, and OPM-2 cells were obtained from American Type Culture Collection (ATCC Virginia, USA); KMS-11, KMS-11/BTZ, and KHYG-1 cells were obtained from the Japanese Collection of Research Bioresources Cell Bank (JCRB Osaka, Japan); MM1.S, ADR-R/RPMI8226 and Dex-R/MM1.S cells were kindly provided by Hiroshi Yasui of the University of Tokyo; OPM-2 and OPM-2/BTZ cells were kindly provided by Masaki Ri and Shinsuke Iida of Nagoya City University; OPM-2 CRBN sh#395, OPM-2 CRBN sh#610, and OPM-2 CRBN KO cells were kindly provided by Junichi Yamamoto, Takumi Ito, and Hiroshi Handa of the Tokyo Medical University.
Reagents
Panobinostat (LBH589), romidepsin, ACY-1215 (ricolinostat), ACY-241, and CUDC-907 were obtained from Selleck Chemicals (Houston, Texas, USA). Each chemical was dissolved in dimethyl sulfoxide (DMSO) and added to the culture medium at the indicated concentrations for in vitro studies. For in vivo experimentation, CUDC-907 was dissolved in DMSO and PEG300, after which Tween80 (polyoxyethylene sorbitan monooleate), and sterile water were added (CUDC-907 5%, PEG300 40%, Tween80 5%, water 50%). Daratumumab for in vitro studies was kindly provided by Janssen Pharmaceutical K.K (Beerse, Antwerpen, Belgium). Elotuzumab was obtained from Bristol-Myers Squibb (New York, New York, USA). Daratumumab and elotuzumab were dissolved in sterile water. CHIR-99021 was obtained from Cayman Chemical Company (Ann Arbor, Michigan, USA).
Western blot analysis and immunoprecipitation
For the preparation of cell lysates, collected cells were washed with PBS and lysed in radio-immunoprecipitation assay (RIPA) buffer containing dithiothreitol, rthylene glycol-bis(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA), protease inhibitors, and phenylmethylsulfonyl fluoride (PMSF). Cell lysates were incubated for 5 min at 4 °C, gently shaken for 30 min at 4 °C, and centrifuged at 20 000 × g for 10 min. The supernatant was collected and used for SDS-PAGE analysis. Western blotting was performed using anti-caspase-3 (Cell Signaling Technology, Danvers, Massachusetts, USA. #9662), anti-cleaved caspase-3 (Cell Signaling Technology, #9661), anti-caspase-7 (Cell Signaling Technology, #9494), anti-cleaved caspase-7 (Cell Signaling Technology, #9491), anti-Ikaros (Cell Signaling Technology, #5443), and anti-Actin (Sigma-Aldrich, St. Louis, Missouri, USA. A4700-2ML) primary antibodies. Primary antibody labeling was detected using Immobilon Forte Western HRP substrate (Merck Millipore, Burlington, Massachusetts, USA). Images were analyzed with a LAS-4000 mini (FUJIFILM, Tokyo, Japan).
Flow cytometry
MM cells were stained with PE anti-human MICA/MICB (BioLegend, San Diego, California, USA: 320906), anti-hULBP-2/5/6 (R&D systems, Minneapolis, Minnesota, USA: FAB 1298P), and PE anti-human CD38 (BioLegend: 356604) antibodies. The cells were analyzed using a BD FACS Verse flow cytometer (BD Biosciences, East Rutherford, New Jersey, USA).
RNA extraction and cDNA synthesis
Total RNA was extracted from MM cells using a RNeasy Mini Kit (Qiagen, Hilden, Germany. 74104). cDNA was synthesized from total RNA using the Super Script III First-Strand Synthesis System (Thermo Fisher, Waltham, Massachusetts, USA. 18080051).
Quantitative reverse transcription PCR (qRT-PCR)
Real-time PCR was performed in triplicate using mRNA obtained from MM cell lines, treated or untreated with HDAC inhibitor for 0, 1, 2, 4 h. Data are expressed as fold change units normalized to 18S ribosomal RNA expression. qRT-PCR experiments were performed using TaqMan Universal Master Mix II, no UNG (Thermo Fisher) and TaqMan Gene Expression Assays for MICA (Hs.130838), MICB (Hs.731446), IKZF1 (Hs.435949), IKZF3 (Hs.4351372), c-Myc (Hs.4331182), and 18 s (Hs.99999901) on a CFX Connect Real-Time PCR Detection System (Hercules, Bio-Rad, California, USA).
ADCC assay
Luciferase-expressing MM cell lines were exposed to HDAC inhibitor or DMSO for 24 h. MM cells were then treated with 0.001, 0.01, 0.1, 1, or 10 µg/mL daratumumab, elotuzumab, or control (IgG) and co-incubated with NK cells. NK cells were extracted from PBMCs obtained from healthy donors using a human NK Cell Isolation Kit (Miltenyi Biotec, Nordrhein-Westfalen, Germany). Cell counting was performed with a hemocytometer (Erma Inc, Tokyo, Japan). NK cells were collected in RPMI 8226 with 10% FBS and 1% penicillin/streptomycin. Fresh NK cells were added at a ratio of 10:1 to MM cells. Cell death was calculated from the decrease in luciferase activity, which was detected by Steady Glo (Promega, Madison, Wisconsin, USA) or PicaGene (TOYO INK, Tokyo, Japan). Luciferase luminescence in the samples was evaluated using a Nivo spectrophotometer (Perkin Elmer, Massachusetts, USA).
Methyl thiazolyl tetrazolium assay
Each MM cell line was seeded in a 96-well plate and incubated with HDAC inhibitors, Akt inhibitor, GSK-3 inhibitor, and PI for 48–72 h. Cells were exposed to lenalidomide and pomalidomide for 5 days, to doxorubicin for 5 h, or to dexamethasone for one week. Methyl thiazolyl tetrazolium (MTT) assays were performed after staining with a Cell Counting Kit-8 (Dojindo Laboratories, Kumamoto, Japan) for 50 min. Plates were read using a Nivo spectrophotometer. MTT assays were performed in quintuplicates.
In vivo animal experiments
Six-week-old C.B-17/Icr-scid/scidJcl mice were purchased from Japan CLEA (Tokyo, Japan). Mice were subcutaneously injected with OPM-2 CRBN-knockout cells to generate SCID mice. After tumor cell injection, SCID mice with tumors over 10 mm in length along the major axis were treated with vehicle or CUDC-907 (50 mg/kg body weight, eight mice per group) three times per week for 2 weeks. The outcome was a change in tumor size compared to the day treatment started. Mice were observed for 14 days after administration. This animal experiment was approved by the Animal Experiment Committee at the Institute of Medical Science of the University of Tokyo (see Study approval). The description was based on The ARRIVE guidelines 2.0 [35].
In vitro experiments using patient samples
Bone marrow samples were collected from MM patients (newly diagnosed or relapse/refractory myeloma). Upon patient consent, an additional 5 mL of bone marrow fluid were collected during a routine bone marrow examination. MM cells were then sorted using FACS Aria (BD Biosciences).
Statistics
For each analysis, P-values < 0.05 were considered to represent statistically significant differences. For qRT-PCR, quantitative data are expressed in box and whisker plots. qRT-PCR was performed in triplicates. Comparisons between two groups were performed by the two-tailed Student’s t-test. For MTT assays, quantitative data are expressed in box and whisker plots. MTT assays were performed in quintuplicates. Statistical analysis between two groups was performed by the two-tailed Student’s t-test. Synergistic effects were evaluated by a generalized linear model including the statistical interaction term of two drugs (distribution: normal. link function: log). Effects on ADCC activity and cell viability were evaluated by a general linear regression model with the statistical interaction term of drugs and log-transformed dose or effector/target (E/T) ratio. Repeated measurements in mice were evaluated by a linear mixed regression model with the statistical interaction term of drugs and time (days), considering intra-individual correlation by including random effects. P-values were calculated for the interaction terms in the regression models, which were interpreted as the difference in slope of dose-/time-dependent change between groups.