Cell lines and cell culture. MDA-MB-231 (HTB-26™), MDA-MB-468 (HTB-132™), PC-3 (CRL-1435™) and NK-92 cells (CRL-2427™) were purchased from the American Type Culture Collection (ATCC) and expanded according to AATC guidelines.
Xenografts. All animal experiments were conducted in compliance with the Animal Care and Use Committee at the University of Michigan. Severe combined immunodeficient (SCID) beige mice (Charles River) were anesthetized intraperitoneally with ketamine (80 mg/kg) and xylazine (5 mg/kg) and injected subcutaneously with either 2×106 luciferase-infected MDA-MB-231 cells or PC-3 cells into the right flank. When tumors reached volumes of 1 cm, mice were infused with 1.5×107 PBMC or 2×106 NK cells via the tail vein. Mice received intraperitoneal injections of UMCD6, anti-PD-1 or IgG control antibodies (100 µg/mouse) every 14 days. Tumor growth was monitored by bioluminescence imaging as described before7.
Generation of MicroOrganoSpheres (MOS). Lung tumor tissue samples were processed, and MOS were generated as described previously11,12. MOS were cultured in medium containing DMEM/F12 (HyClone), HEPES (Gibco) and Glutamax (Gibco Life Technologies) and dosed on day 2 with anti-PD1, UMCD6 and controls for 4 days. Annexin V green dye was used to indicate cell death and longitudinal images were taken in the Incucyte®.
Isolation of human peripheral mononuclear cells (PBMC) and NK cells. PBMCs were isolated by density gradient centrifugation using Ficoll-Paque (GE Healthcare) from healthy volunteers. NK cells were isolated using the EasySep® Human NK Cell Isolation Kit (STEMCELL Technologies) per manufacturer’s instructions.
RNAseq analysis. Bulk RNA-seq was performed by Novogene. A total of 6 samples were used for these experiments. To prepare these samples, total RNA from NK-92 cells treated with 10 µg/ml of UMCD6 or IgG for 6 hours was extracted using RNAeasy MiniPrep Kit (Qiagen). Samples were then sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. Differential gene expression analysis was performed using DESeq2. P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and log2 (Fold-change) of 1 were set as the threshold for significantly differential expression.
RT-PCR analysis. NK-92 cells were treated with 10 µg/ml of UMCD6 and harvested at 6 hours. RNA was extracted using Direct-zol RNA MiniPrep (Zymo Research). mRNA expression was measured using SYBR Green PCR Master Mix Reagent (Thermo Fisher Scientific) and the following primers: NKG2D F: 5′-TTCAACACGATGGCAAAAGC-3′, NKG2D R: 5′-CTACAGCGATGAAGCAGCAGA-3′, HCST F: 5'-TCTGGGTCACATCCTCTTCCT-3' and HCST R: 5'-AAGTGCCAGGGTAAAAGGCAG-3'). Real abundance was calculated using the ΔΔCT method on a ViiA V.7 Real-Time PCR System (Applied Biosystems).
Western blotting. NK-92 cells were treated with UMCD6 or an IgG control antibody at 10 µg/ml and cell lysates were collected after 72 hours. To measure changes in PI3K and mTOR expression, HRP-conjugated antibodies to PI3K (Cell Signaling, Cat#428T), and mTOR (Cell Signaling, Cat#2972) were used at 1:1000 in 5% milk. β-actin (Cell Signaling, Cat#13E5) was used control for loading. Bands were imaged on an Amersham Imager 600RGB (GE Healthcare).
Antibodies. Pembrolizumab and nivolumab (anti-PD-1) were obtained from Merck and Bristol-Myers Squibb. The following antibodies were used for flow cytometry analyses: FITC anti-human CD4 (BioLegend Cat#391503), PE anti-human CD45 (Biolegend, clone HI30), APC anti-human CD56 (Biolegend, clone 5.1H11), APC/Cyanine7 anti-human CD8a (Biolegend, San Diego, CA, USA, clone RPA-T8), PE/Cyanine7 anti-human CD3 (Biolegend, clone HIT3a), PerCP/Cyanine5.5 anti-human CD314 (NKG2D) (Biolegend, clone 1D11), FITC anti-human CD6 (Biolegend, clone BL-CD6), APC anti-human CD16 (Biolegend, clone 3G8), Pacific Blue anti-human/mouse Ki67 (Biolegend, clone 16A8), FITC anti-human/mouse Granzyme B (Biolegend, clone GB11) and APC anti-human Perforin (Biolegend, clone B-D48).
Immunohistochemistry. Xenograft tumors derived from breast cancer MDA-MB-231 cells were embedded in optimal cutting temperature compound (Sakura Finetek) for cryosectioning at 8 µm. Antibodies against CD56 (Biolegend, clone 5.1H11) were incubated at 1:100 dilutions overnight. The following day, slides were incubated with goat anti-mouse IgG-Cy3 antibodies (Jackson ImmunoResearch) for 1 hour at room temperature. Fluorescence images were taken using an Olympus BX51 microscope (Olympus America Inc.).
Statistical Analysis. The statistical analysis for all the experiments was performed using Graph Pad Prism software (GraphPad Prism). Bioluminescence, RT-PCR and western blot data are shown as mean ± standard error of the mean and statistical significance between two groups (for normally distributed data) was determined by the unpaired Student’s t test. ANOVA was used for not normally distributed data.