Cell Lines
PCa cell lines, PC3 and LNCaP, were from the American Type Culture Collection (Manassas, VA, USA, Cat# CRL-1435, and CRL-1740, respectively) and cultured in RPMI-1640 medium (Corning, Corning, NY, USA Cat# 10-040-CM), supplemented with 10% (v/v) fetal bovine serum (FBS, Corning, Corning, Cat# MT35010CV), penicillin/streptomycin (Corning, Cat# 30-002-CI), and normocin 1G (Invivogen, San Diego, CA, USA, Cat# NC9390718). Cells were grown under 5% CO2 at 37°C. Short tandem repeat service provided by ATCC (Cat# ATCC-135-XV) was used to authenticate the cell lines. Mycoplasma testing was conducted at least twice a year using the Lonza MycoAlertTM Mycoplasma Detection Kit (Lonza, Basel, Switzerland, Cat# LT07-218).
Antibodies
Rabbit antibodies targeting the following proteins were acquired from Cell Signaling Technology (Danvers, MA, USA): CYR61 (D4H5D) (Cat# 14479S), α/β-tubulin (Cat# 2148S), β-actin (13E5) (Cat# 4970), Phospho-AKT (Thr308) (Cat# 2965), Phospho-p44/42 MAPK (Erk1/2) (Cat# 9101S). Mouse monoclonal antibodies included CYR61 (A-10) (Santa Cruz Biotechnology, Dallas, TX, USA, Cat# sc-374129).
Immunoblotting
Whole-cell lysates were prepared by lysing the cell pellet in 100 µL Invitrogen™ Cell Lysis Buffer II (Thermo Fisher Scientific, Waltham, MA, USA Cat # FNN0021) on ice for 30 minutes, vortexing at 10 minutes intervals. The cell lysis buffer was supplemented with 1 mM Thermo Scientific™ PMSF Protease Inhibitor (Thermo Fisher Scientific, Cat# PI36978) and Halt™ Protease and Phosphatase Inhibitor Cocktail (Thermo Fisher Scientific, Cat# P178440). The cell extract was centrifuged at 13,000 rpm for 10 minutes at 4°C. The supernatant was collected, and protein concentration of the lysates was determined using the Pierce™ BCA Protein Assay Kit (Thermo Fisher Scientific, Cat# 23225) to ensure equal loading of proteins separated on individual lanes by SDS-PAGE (NuPAGE 4–12%, Thermo Fisher Scientific, Waltham, MA, USA). Samples for immunoblot analysis were diluted in ultrapure water, Invitrogen™ 1× Bolt™ Sample Reducing Agent (Thermo Fisher Scientific, Cat# B0004), and Invitrogen™ NuPAGE™ Lithium Dodecyl Sulfate Sample Buffer (1×) (Thermo Fisher Scientific, Cat# NP0007) to a concentration of 50 µg of protein per 20 µL, then heated at 70°C for 10 minutes. Electrophoresis was followed by protein transfer to polyvinyl difluoride membranes (Millipore Sigma, Burlington MA, USA, Cat# IPFL00010). Membranes were blocked for one hour at room temperature with Intercept® Blocking Buffer (Li-Cor, Lincoln, NE, USA Cat# 927-60001) and probed overnight with appropriate primary antibodies. Membranes were then washed with TBS-Tween buffer (20 mM Tris-HCL, pH 7.6, 140 mM NaCl, and 0.2% Tween 20) three times for 5 minutes each. After washing, membranes were incubated with IRDye® 680RD Goat anti-Rabbit IgG Secondary Antibody (Licor, Cat# 926-68071) or IRDye® 680RD Goat anti-Mouse IgG Secondary Antibody (Licor, Cat# 926-68070). Washes were repeated after secondary antibody incubation. Membranes were imaged using a Li-Cor Odyssey scanner. Protein bands from at least 3 independent blots were scanned for each protein of interest, quantified using ImageJ software (National Institutes of Health, Bethesda, MD, USA, Fiji Version 1.44a), and normalized to α/β-tubulin or β-actin loading control protein bands to determine fold upregulation.
Cell viability assay
Trypan blue dye exclusion assay was employed to assess the effects of CYR61 siRNA on the viability of PC3 and LNCaP cells. Following siRNA transfection, cells (both floating and adherent) were collected, pelleted by centrifuging at 1500 rpm for 5 minutes, and resuspended in 1 mL 1× phosphate-buffered saline (PBS). After pellet resuspension, 10 µL of cell suspension was combined with 10 µL trypan blue (Thermo Fisher Scientific, Cat# MT25900CI), and live cells were counted using a Cellometer Vision CBA Image Cytometer (Nexcelom, San Diego, CA, USA). Cell viability was expressed as a percentage of the viability of the scrambled small interference RNA (siRNA) duplex (SD) control.
The CellTiter-Glo® assay was used to assess cellular proliferation and viability. Following CYR61 siRNA transfection, PC3 and LNCaP cells were seeded (5000 cells/well) in opaque-walled 96-well plates (Thermo Fisher Scientific, Cat# 12-566-620) and 100 µL complete media. Control wells containing medium without cells were used to determine background luminescence. Cells were assessed for 1 to 4 days post-transfection. After each time point, a volume of CellTiter-Glo® 2.0 Reagent equal to the volume of cell culture medium present in each well (100µl) was mixed for 2 minutes on an orbital shaker to induce cell lysis. Following this, the plate was incubated at room temperature for 10 minutes to stabilize the luminescent signal. The luminescence was recorded using an integration time of 0.25–1 second per well per manufacturer’s instructions.
RNA Interference
PC3 and LNCaP cells (50,000 cells per well) were cultured on 6-well plates and transfected after 24 hours with either 50 nM or 100 nM siRNA for up to 96 hours. The siRNA sequences used were as follows: si-CYR61 knockdown (KD, pool of three different siRNA duplexes from Santa Cruz Biotechnology, Cat# sc-39331). Cells were transfected using Interferin® siRNA transfection reagent (Polyplus-transfection®, Illkirch, France, Cat# 409-01). Scrambled siRNA duplex (SD, Dharmacon, Lafayette, CO, USA, Cat# D-001210-0105) was used as a non-targeting negative control. Protein depletion was assessed by immunoblotting.
Clonogenic Assay
PC3 and LNCaP cells were transfected with CYR61 siRNA and grown in RPMI-1640 medium supplemented with 10% FBS for 72 hours. Next, an equal number of viable transfected cells was transferred to 6-well culture plates (500 cells/well for PC3 and 1000 cells/well for LNCaP). Colony formation plates were incubated for 10 days at 5% CO2 and 37°C. Adherent colonies were washed with 1× PBS, fixed with 3:1 (v/v) methanol:acetic acid solution for 5 minutes, washed again with 1× PBS, stained with 0.5% crystal violet for 20 minutes, and then washed gently with tap water. Images of the stained colonies were acquired using a Li-Cor Odyssey scanner and quantification was performed using the automated colony counting capability of Image J software following identical parameters for each well.
Prostasphere Formation Assay
Spheroid cultures from siRNA transfected cells were maintained using complete MammoCult™ medium (Stem Cell Technologies, Vancouver, Canada, Cat# 05620) supplemented with hydrocortisone (0.48 g/mL, Millipore Sigma-Aldrich, Cat# H0135), heparin (4 g/mL Sigma-Aldrich, St. Louis, MO, USA, Cat# H3149), and 1% penicillin/ streptomycin. PC3 and LNCaP cells were seeded at 50,000 cells per well and transfected with the various siRNAs. After 48 h, an equal number of viable cells (1000 cells/well) were harvested and resuspended 50 times in MammoCult™ medium to ensure a single-cell suspension. Cells then were seeded in 24-well untreated plates (Genesee Scientific, Morrisville, NC, Cat# 25–102) in 0.5 mL MammoCult™ medium. Prostaspheres were grown for 10 days at 37°C/5% CO2 and visualized in a Zeiss Observer II microscope. The prostasphere area was quantified from three independent images per individual treatment using Image J software.
Wound Healing Assay
PC3 and LNCaP cells were examined for their mobility using a wound-healing assay. Following CYR61 siRNA transfection for 72 hours, cells were collected and seeded into a 24-well plate (Thermos Fisher Scientific, Cat# 09-761-146) to reach semi-confluency. Confluent transfected cells were “scratch wounded” with a P200 pipette tip. Wound closure was monitored by a Nikon Eclipse Ti microscopy. Images were taken every 12 hours over 48 hours and analyzed with ImageJ software. The average wound area relative to the initial wounding (0 hr) was determined in three independent triplicate assays and compared to control cells transfected with SD negative control.
IGF1 Induction Treatment
To determine if IGF1 increased the expression of CYR61, PC3, and LNCaP cells were induced with 100 ng/ml recombinant human IGF1 (Peprotech, Cranbury, NJ USA Cat# 100 − 11) for 30 minutes, 4 hours, and 24 hours. CYR61 protein expression levels were measured at different time points. Experimental cells were plated, and once cells reached 70% confluence, they were switched to serum-free media with 0.1% BSA for overnight starvation. Immediately after exposure to IGF1 for the designated time, the cells were collected for protein extraction or evaluated for expression.
In-Cell Western (ICW) Assay
The ICW assay was performed using the Odyssey Imaging System (LI-COR Biosciences, Lincoln, NE, USA) according to the manufacturer's instructions. PC3 and LNCaP cells were grown in 96-well plates until they reached 60–70% confluency and then fixed with 4% paraformaldehyde at selected time intervals post-transfection or IGF1 induction for the ICW assay. Then, cells were permeabilized with 0.5% Triton X-100 for 15 minutes at room temperature and blocked with LI-COR Odyssey Blocking Solution (LI-COR Biosciences) for 30 minutes. The cells were incubated at 4°C overnight with appropriate primary antibodies. After three washes with 1× PBS, cells were stained with secondary antibodies at room temperature for 2 hours. The plates were scanned with the Odyssey CLx Infrared Imaging System (LI-COR Biosciences), and the integrated fluorescence intensities representing the protein expression levels were acquired using the software provided with the imager station (Empiria Studio 2.3, LI-COR Biosciences). The relative amount of protein was obtained by normalizing to endogenous β-actin or α/β-tubulin in all experiments.
Transwell Migration Assay
Cell migration was assessed using 24-well ThinCert™ (Greiner Bio One, Frickenhausen, Germany, Cat#662638) permeable inserts containing PET capillary pore membranes with 8.36 mm inner diameter, 10.34 mm outer diameter, 16.22 mm height, and 8 µm pore size. The assay was carried out once the transfection time ended. PC3 and LNCaP cells were trypsinized and 1 × 105 live cells/ml were re-suspended in serum-free RPMI medium. While the cell suspensions were prepared, 500 µl of the chemoattractant (RPMI supplemented with 10% FBS) was dispensed into each well of the 24-well ThinCert™ plates and incubated at 37°C for 1 h. The ThinCert™ inserts were placed in the wells containing pre-warmed chemoattractant, and 1 × 105 live cells/ml (200 µl from the cell suspension) were applied. Subsequently, the plates were incubated at 37°C for 48 h. The medium in the inserts was then removed and the membranes were washed twice in PBS. The PC3 and LNCaP cells that remained in the upper part of the insert were removed carefully with a PBS-soaked cotton swab. The cells that migrated or invaded towards the lower part of the chamber were fixed with 4% formaldehyde and stained with 0.5% crystal violet. The fixed cells were visualized on a Zeiss Observer II microscope and photographed. The total number of cells that migrated or invaded was counted manually using ImageJ software.
Statistical Analysis
Data are expressed as mean ± SEM from a minimum of three independent experiments. Statistical analysis was performed with GraphPad Prism version 9 (GraphPad Software, San Diego, CA, USA). Two-sample comparisons were determined using the two-tailed Student t-test. For multiple groups, we used two-way ANOVA. The p values < 0.05 were considered statistically significant.