Materials
All chemokines were obtained from PeproTech (Rocky Hill, NJ, USA). The NanoBiT starter kit, containing the plasmids and all reagents for the protein interaction assay, was from Promega (Madison, WI, USA). The pBiT3.1 plasmid, pGlo22F plasmid, and all reagents for these plasmid-related assays were also purchased from Promega. The pcDNA3.1 expression vector was purchased from Invitrogen (San Diego, CA, USA). The SRE-Luc vector which contains four copies of the serum response element (SRE; CCATATTAGG) was acquired from Stratagene (La Jolla, CA, USA). Anti-HA antibodies and agarose beads conjugated with anti-FLAG antibodies were from Sigma-Aldrich (St. Louis, Mo, USA). Anti-ERK (cat. no. 4695) and anti-pERK (Thr202/Tyr204) (cat. no. 4370) antibodies were from Cell Signaling Technology (Beverly, MA, USA). Anti-GFP (cat. no. sc-8432), anti-β-actin (cat. no. sc-9996), and all secondary antibodies were from Santa Cruz Biotechnology (Santa Cruz, CA, USA). All primers for gene cloning and PCR and related materials were obtained from Cosmo Genetech Co., Ltd. (Seoul, Korea), and the DNA sequencing was conducted by Macrogen (Seoul, Korea). Unless otherwise stated, all reagents were purchased from Sigma-Aldrich.
Cell culture
HEK293 and HeLa cells were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). All cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 IU/ml penicillin G, and 100 μg/ml streptomycin (Invitrogen, Carlsbad, CA, USA). Gα12/13-knockout HEK293 cells were a kind gift from Professor Asuka Inoue, Tohoku University.
Plasmid construction
The CMV promoter sequence in pcDNA3.1 vector was substituted with promoters from the Ubiquitin C gene (UbiC) or HSV-TK gene (HSV-TK) to develop a regulated expression system. CXCR4, CXCR7, and GFP genes were inserted into these vectors. The fragments of Nano-Luciferase gene in NanoBiT vectors from the company were inserted into a multicloning site in UbiC. All genes for the NanoBiT assay were constructed as N-terminal or C-terminal tagged forms in the vector containing the UbiC promoter. The chimeric receptor genes were generated by overlap PCR using primers and inserted into the NanoBiT vector. Either the CXCR4 or CXCR7 gene was inserted into the FG12 vector to generate lentivirus.
RT-PCR
Total RNA was extracted from cells using TRIzol (Invitrogen) according to the manufacturer’s instructions. Next, 3μg of RNA was reverse transcribed using M-MLV Reverse transcriptase to generate cDNA (Promega, Madison, WI, USA). The PCR reaction mixture contained cDNA in the presence of Taq DNA polymerase, buffer, dNTPs and primer pairs. The primer pairs for the housekeeping gene beta-actin (Forward: 5’-AGAAAATCTGGCACCACACC-3’; Reverse: 5’-CCATCTCTTGCTCGAAGTCC-3’) generated PCR products of 435 bp. The human CXCR7 primers (Forward: 5’-CAGCAGAGCTCACAGTTGTTG-3’; Reverse: 5’-GAGCAGGACGCTTTTGTTGG-3’) and human CXCR4 primers (Forward: 5’-GGCCAGCCAGCACCTATTTG-3’; Reverse: 5’-TGGCTTTGCCCCCTTGAAA-3’) amplified fragments of 269 bp and 254 bp, respectively. The PCR reaction was performed on a thermal cycler (SimpliAmp Thermal Cycler, Thermo Fisher Scientific) using the following conditions: 95°C, 5 minutes; 30 cycles (95°C, 30 seconds; 58°C, 30 seconds; 72°C, 40 seconds); 72°C, 7 minutes. PCR products were separated on a 2% agarose gel by electrophoresis and imaged.
Structural complementation assay based on NanoBiT technology
HEK293 cells were seeded into 96-well microplates at the density of 2.0 × 104 cells/ well. The next day, 50 ng of receptor plasmid (receptor fused with LgBiT or SmBiT) and 50 ng of β-arrestin2 plasmid (attached with SmBiT or LgBiT in N-terminal or C-terminal) were mixed with 0.2 μl Lipofectamine 2000 (Invitrogen, Carlsbad, CA) and added to the cells. The other steps of transfection were carried out following the manufacturer’s instructions. This formulation was used for all the other two-gene combinations. For three-gene combinations, 30 ng of each gene preparation was used for transfections. 24 h later, before measuring luminescence, cells were stabilized for 10 min at room temperature by replacing the media with 100 μl of Opti-MEM. Then, 25 μl Nano-Glo Live Cell Reagent (furimazine) was added to each well, and baseline luminescence was measured for the first 10 min. Finally, cells were stimulated using 10 μl of SDF-1α or I-TAC at a concentration of 100 ng/ ml, and cell-plate measurements were continued for 1 h. These procedures were conducted using a luminometer (BioTek Instruments, Inc., Winooski, VT, USA).
HiBiT assay
The expression of receptors on cell membranes was detected using the Nano-Glo HiBiT extracellular system (Promega, Madison, USA). HEK293 cells were seeded into 96-well plates at a density of 2.0 × 104 cells per well. The next day, cells were transfected with a mixture of DNA constructs of SmBiT-receptors: pBiT3.1N (0.5 ng, 5 ng, or 50 ng) and 0.2 μl of Lipofectamine 2000. After 24 h, 100 μl of Nano-Glo HiBiT extracellular reagent (1 μl of LgBiT protein + 2 μl substrate + 97 μl of Nano-Glo HiBiT buffer) was added to each well. The assay plate was then left to equilibrate for 4 min at room temperature without mixing. Luminescence values were measured using the Synergy 2 Multi-Mode Microplate Reader (BioTek, Winooski, VT, USA).
Cellular imaging
HEK293 cells were seeded onto poly-L-lysine-coated cover glasses. The next day, cells were transfected with plasmids containing receptors in different forms or β-arrestin2-GFP by Lipofectamine 2000. SDF-1α was applied to the cells for 30 min after overnight starvation. After washing with PBS, cells were fixed, and GFP signals were observed using a LSM800 confocal microscope (Carl Zeiss Microimaging Inc., Zena, Germany). For pulse labeling of surface receptors described previously [41], cells expressing HA-tagged receptors were kept at 4°C for 60 min after the medium was replaced by ice-cold Opti-MEM (Invitrogen) containing anti-HA antibodies. Cells were washed with PBS and incubated with Opti-MEM containing SDF-1α at 37°C for 30 min to allow receptor internalization. Then, cells were fixed, permeabilized, and HA signals were detected using FITC-conjugated goat anti-mouse IgG. Images were obtained using the confocal microscope.
Immunoprecipitation and western blot analyses
Cells were lysed by adding lysis buffer (150 mM NaCl, 50 mM Tris-HCl pH 7.5, 10 mM KCl, 1% Triton X-100, 10 mM NaF, 5 mM Na3VO4) complemented with protease inhibitor cocktail (Roche, Indianapolis, IN, USA). Protein quantification was performed using a Bradford protein assay kit (Bio-Rad, Hercules, CA, USA). Cell lysates were then denatured with SDS sample buffer and an equal amount of protein was separated on 10% polyacrylamide gels and then transferred to nitrocellulose membranes for immunoblotting. The membranes were blocked with 5% nonfat dry milk in Tris-buffered saline with Tween 20 (TBST) and probed with appropriate antibodies. Finally, the signal by HRP-conjugated secondary antibodies was developed using an enhanced chemiluminescence (ECL) kit (GE Healthcare Life Sciences, Marlborough, MA, USA).
For immunoprecipitations, HEK293 cells were transfected with HA-tagged CXCR4 or CXCR7. 36 h after transfection, cells were washed with cold PBS and lysed with lysis buffer containing protease inhibitor cocktail (Roche). For the cross-linking experiments, cells were washed with PBS twice and incubated with PBS containing 2 mM Bissulfosuccinimidyl substrate (BS3) for 30 min. The reaction was stopped by adding Tris-buffered saline, and cells were then washed again with the same buffer and lysed with lysis buffer. The lysates were centrifuged, and the supernatants were incubated with anti-FLAG antibody-conjugated beads. The beads were washed at least four times with the lysis buffer and the bound proteins in SDS sample buffer were subjected to SDS-PAGE, followed by immunoblotting with the appropriate antibodies.
cAMP assay
HEK293 cells were seeded into 96-well microplates at a density of 2.0 × 104 cells/well. The next day, 60 ng of pcDNA3.1/ CXCR7 or pcDNA3.1/ CXCR4 and 40 ng of pGlo22F plasmid were added to each well. The plate was incubated in the 5% CO2 incubator at 37°C to let proteins express for 36 h. Before performing the assay, cells were incubated in equilibration medium containing 10% v/v dilution of the Glosensor cAMP reagent stock solution using CO2--independent medium. After 1 h of incubation, cells were stabilized for 10 min at RT. Cells were treated with vehicle or 100 ng/ ml SDF-1α. After 10 min, isoproterenol was added at 10 μM following by luminescence measurement for 50 min. Luminescence values were measured using the Synergy 2 Multi-Mode Microplate Reader (BioTek, Winooski, VT, USA).
Detection of intracellular calcium increase
We developed new method to measure intracellular calcium change using NanoBiT technology (manuscript accepted). HEK293 cells stably expressing Gαqi chimera were seeded in 96-well plates at a cell density of 2´104 cells/well. The next day, 30 ng of receptor plasmids, 30 ng of plasmids containing calmodulin tagged with SmBiT at C-terminal, and 30 ng of plasmids containing MYLK2S fused to LgBiT at the N-terminal were mixed with 0.2 ml Lipofectamine 2000 (Invitrogen, Carlsbad, CA) and added to the plated cells. Following transfection steps were performed according to the manufacturer’s instructions. After 24 h, media was replaced with 100 ml of Opti-MEM and cells were stabilized for 10 min at room temperature before measuring the luminescence. Then, 25 ml of Nano-Glo Live Cell Reagent (furimazine) was added to each well, and basal luminescence was measured using a luminometer (BioTek Inc., Winooski, VT, USA) for the first 10 min. Finally, cells were stimulated by adding 10 ml of SDF-1α at a final concentration of 100 ng/ ml to each well, and the real time change of luminescence was measured for 30 min.
Reporter gene assay
HEK293 cells exogenously expressing Gαqi construct were seeded into 48-well plates at a density of 2.5 × 104 cells/well. The next day, a mixture of 75 ng of pcDNA3.1/CXCR7 (or pcDNA3.1/CXCR4, pcDNA3.1/CXCR3), 75 ng of SRE-Luc reporter gene plasmids, and 0.3 μl of Lipofectamine 2000 was added per well, according to the manufacturer’s instructions. The next day, cells were maintained in serum-free DMEM overnight. After approximately 36 h since transfection, the cells were treated with SDF-1α (100 ng/ml), I-TAC (100 ng/ml), or VUF11207 (100 nM) for 6 h. Cells were then lysed with 100 μl of lysis buffer, and the luciferase activity of cell extracts was measured using a luciferase assay system, following the standard protocol for the Synergy 2 Multi-Mode Microplate Reader (BioTek Inc., Winooski, VT, USA)
Establishment of knockout cells by CRISPR-Cas9
To establish cells lacking receptors, four potential target sequences for each gene were chosen using a guide design program from the Zhang Lab (https://zlab.bio/guide-design-resources). The two-strand oligos were annealed and inserted into the pRG2 vector, and 49 nucleotides including the target site were inserted into the pMRS surrogate vector. These two vectors were introduced into HEK293 cells with p3S-Cas9 plasmids and examined guide efficiency by genomic DNA PCR with appropriate primers and T7E1 treatment. The efficient guide vectors (CXCR4: TACACCGAGGAAATGGGCTCAGG, CXCR7: GGAACTTCTCGGACATCAGCTGG), surrogate vector, and p3S-Cas9 were transfected into the cells. Potential gene knockout cells were isolated by MACSelect Kk MicroBeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and transferred to 96-well plates at 0.5 cells/ well. Gene deletion was confirmed by genomic DNA PCR and T7E1 analysis. PCR products were inserted into pGEM-T easy vector. After transformation, the isolated DNAs from 10 clones of E. Coli were sequenced to confirm gene modification.
Growth assay
HeLa cells (2,000 cells/well) lacking each of the receptors were seeded into 4 different 96-well plates containing complete media for 24 h. After every 24 h, cells in each plate were incubated with 10 μl of CCK-8 solution for 2 h, and the absorbance of each well was then measured at 450 nm using a microplate reader. Cell growth was measured using the Cell Counting Kit-8 (CCK-8) from Dojindo Molecular Technologies, Inc. (Rockville, MD, USA) following the manufacturer's instructions.
Migration assay
HeLa CXCR4 KO and CXCR7 KO cells were first infected with FG12/CXCR4 or FG12/CXCR7 virus supernatants using 5 μg/ml polybrene. Chemotaxis assays were performed by using transwell plates with 8-μm pore size (Corning Inc. Corning, NY, USA). The inserts were filled with 2.5 × 104 cells in 100 μl serum-free DMEM. For the lower wells, 650 μl of serum-free DMEM with SDF-1α (50 ng/ml) was added. The cells were kept in a 37°C incubator containing 5% CO2. After 24 h, non-migrated cells in the upper chamber were removed by a wet cotton swab. Cells that migrated were fixed with 4% paraformaldehyde, stained using hematoxylin and eosin, and then counted in four high-power microscope fields (100×).
U937 cells infected with FG12/CXCR7 virus were applied to the chemotaxis assay. The upper wells of transwell plates (8-μm pore size) was filled with 2.5 × 104 cells in 100 μl serum-free RPMI, and the lower wells were filled with 650 μl of serum-free RPMI containing different concentrations of SDF-1α. After 6 h, cells that had migrated to the lower wells were counted using a hemocytometer.
Statistical analysis
Unpaired Student’s t-tests or ANOVA using PRISM5 software (GraphPad; La Jolla, CA, USA) were used for statistical analyses. Group means were further analyzed using Bonferroni’s multiple-comparison tests. The data were presented as the mean ± SD, and all experiments were performed as triplicates, unless otherwise indicated