2.1. Antibodies and reagents
The following antibodies were used in this study: β-actin (Sigma-Aldrich, clone AC-74), FGFR1 (Santa Cruz Biotechnology, sc-121), FGFR2 (Cell Signaling, #23328), integrin β1 (Cell Signaling, #4706; Santa Cruz Biotechnology, sc-9970), integrin α1 (Santa Cruz Biotechnology, sc-10728), integrin α2 (Santa Cruz Biotechnology, sc-9089), integrin α3 (Santa Cruz Biotechnology, sc-6592), integrin α5 (Chemicon International, AB1949), integrin α6 (Cell Signaling, #3750), LAMP1 (R&D Systems, MAB4800), DyLight™ 488-conjugated AffiniPure Goat Anti-Rabbit (Jackson ImmunoResearch), AlexaFluor® 680-conjugated AffiniPure Goat Anti-Rabbit (Jackson ImmunoResearch), DyLight™ 594-conjugated AffiniPure Donkey Anti-Mouse (Jackson ImmunoResearch), AlexaFluor® 790-conjugated AffiniPure Donkey Anti-Mouse (Jackson ImmunoResearch), Mouse Anti-Goat IgG-HRP (Santa Cruz Biotechnology, sc-2354). Leupeptin (Sigma-Aldrich) and MG-132 (Selleckchem) were used as inhibitors of lysosomal proteases and proteasome, respectively. For 3D cultures, adhesion assay, cell-spreading assay and migration assay the following extracellular matrix proteins were used: growth factors reduced Matrigel® Basement Membrane Matrix (Corning), rat tail Collagen type I (Millipore) and Fibronectin (Bio-Rad).
2.2. Cell culture
HB2 cells were purchased from ECACC, grown in DMEM (Corning) supplemented with 10% FBS (Biowest), 5 µg/ml insulin, 5 µg/ml hydrocortisone, 100 U/ml penicillin and 100 µg/ml streptomycin (HyClone), and passaged for a maximum of 2–3 months after reconstitution. Cells were routinely tested for mycoplasma contamination.
2.3. Knock-down of FGFR2
HB2 cells with stable knock-down of FGFR2 were established with shRNA-based lentiviral construct as previously described [19, 22]. HB2 FGFR2(-) cells were maintained in a medium supplemented with 0.2 µg/ml puromycin (Sigma-Aldrich). In all experiments, respective cells transfected with empty vector were used as controls. The stability of silencing of FGFR2 was verified by immunoblotting before each set of experiments.
2.4. Western blotting
Cells grown to 70–80% confluence were scraped in ice-cold PBS and lysed in Laemmli buffer (2x concentrated) supplemented with 2 mM PMSF, 10 µg/ml aprotinin, 10 µg/ml leupeptin, 5 mM EGTA, 1 mM EDTA, 2 mM Na4P2O7, 5 mM NaF and 5 mM Na3VO4. An equal amount of protein (~ 20 µg) per lane was loaded, resolved in SDS-PAGE and transferred onto a nitrocellulose membrane. The membranes were blocked in 5% skimmed milk and incubated overnight with specific primary antibodies at 4ºC. Secondary antibodies conjugated with AlexaFluor® 790 or AlexaFluor® 680 (from Jackson ImmunoResearch) and Odyssey Clx system or secondary antibodies conjugated with horseradish peroxidase (Sigma-Aldrich) and Western Lightning Plus-ECL (PerkinElmer) were used for visualisation of detected proteins. Densitometry of bands representing detected proteins was done with Image StudioTM Software Ver 5.2 (Odyssey CLx).
2.5. Three dimensional cell cultures
1×103 HB2 or HB2 FGFR2(-) cells were resuspended in 40 µl (1:1 ratio) of growth factor reduced Matrigel® Basement Membrane Matrix or 0.8 mg/ml of rat tail Collagen type I and cultured in an embedded culture for 8 days. For morphological analyses representative pictures were taken using ZEISS PrimoVert microscope.
2.6. MTT proliferation assay
HB2 and HB2 FGFR2(-) cells were seeded into 96-well plate in triplicates. After 72 h the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT, Sigma-Aldrich) was added into each well (0.5 mg/ml) and incubated for 2h at 37ºC. Then the medium was discarded and formazan crystals were dissolved in DMSO for 15 minutes at room temperature (RT). The absorbance was measured at 590 nm using microplate reader (BioTek).
2.7. Adhesion assay
HB2 and HB2 FGFR2(-) cells were seeded into fresh 60-mm cell culture dishes the day before an assay. A 96-well plate was coated with 100 µg/ml of freshly prepared Matrigel® Basement Membrane Matrix, rat tail Collagen type I or Fibronectin overnight at 4ºC. Coating with 100 µg/ml of BSA (Carl Roth) was used as a control. Next, cells were detached with enzyme-free cell dissociation buffer EDTA-based (Millipore) and stained with 10 µM 2',7'-Bis-(2-Carboxyethyl)-5-(and-6)-Carboxyfluorescein, Acetoxymethyl Ester (BCECF, AM; ThermoFisher) for 15 minutes at RT, protected from light. After washing step, cells were resuspended in serum-free medium and seeded into pre-coated wells (5 × 104 cells per well). Cells were allowed to attach for 90 minutes at 37ºC. After 3–5 washing steps with PBS, fluorescence signal of the attached cells was measured using microplate reader (excitation wavelength at 439 nm, emission wavelength at 535 nm).
2.8. Cell-spreading assay
HB2 and HB2 FGFR2(-) cells were seeded into fresh 60-mm cell culture dishes the day before an assay. Coverslips were coated with 100 µg/ml of freshly prepared Matrigel® Basement Membrane Matrix, rat tail Collagen type I or Fibronectin overnight at 4ºC. Coated coverslips were washed with PBS and blocked with 1 mg/ml BSA for 30 minutes. Next, cells were detached with enzyme-free cell dissociation buffer EDTA-based, seeded onto coated coverslips in 12-well plate and allowed to attach and spread for 90 minutes at 37ºC. After washing with PBS, cells were fixed in 4% paraformaldehyde (PFA) at RT, permeabilised with 0.1% Triton X-100 at 4°C and mounted with Vectashield® HardSet™ Antifade Mounting Medium with Phalloidin (Vector Laboratories). The extent of cell spreading was quantified as an area of phalloidin signal per cell using ImageJ software. Representative images were taken using ZEISS AxioVert fluorescent microscope.
2.9. Migration assay
Transwell migration assay was performed as previously described [23]. Briefly, HB2 and HB2 FGFR2(-) cells were seeded into 60-mm cell culture dishes the day before an assay. Next, cells were detached with enzyme-free cell dissociation buffer EDTA-based, resuspended in serum-free medium and 2 × 105 cells were placed in the inner compartment of the Boyden chamber inserts (8 µm pores, BD Bioscence), coated with 100 µg/ml of freshly prepared Matrigel® Basement Membrane Matrix, rat tail Collagen type I or Fibronectin. Cells were allowed to migrate towards the complete medium (10% FBS) for 24 hours at 37ºC. The following day, non-migrated cells were removed using a cotton swab. Nuclei of migrated cells were stained with Hoechst and porous membranes were mounted onto glass slides for further analyses using ZEISS AxioVert fluorescent microscope. Migrated cells were counted from 20 random fields and representative images were taken.
2.10. Immunofluorescence
2 × 104 HB2 and HB2 FGFR2(-) cells per well of an 8-well Millicell slide (Millipore) were seeded in 400 µl of complete culture medium and incubated for 24 hours at 37ºC. Next day, after fixation with 4% PFA for 10 minutes at RT, permeabilisation with 0.1% Triton X-100 at 4ºC and blocking with blocking buffer (3% BSA, 3% FBS in PBS) for 1 hour at RT, cells were incubated with the desired concentrations of primary antibodies diluted in blocking buffer, overnight at 4ºC. Secondary antibodies conjugated with DyLight™ 488 or DyLight™ 594 (from Jackson ImmunoResearch) together with a counterstain for the nucleus with Hoechst were used for the visualisation of desired target proteins using scanning confocal microscope Leica HCS LSI (Leica).
2.11 RNA isolation, cDNA synthesis and RT-qPCR
Total RNA was isolated with TriPURE reagent (Roche) according to manufacturer’s protocol. cDNA was synthesised using the Transcriptor cDNA First Strand Synthesis Kit (Roche). For analysis of ITGB1 gene expression TaqMan probe Hs00559595_m1 was used. TaqMan probes for ACTB (Hs99999903_m1) and GAPDH (Hs02786624_g1) were used as reference genes. For qPCR reaction, TaqMan Universal PCR Master Mix (Applied Biosystem) was used. Reactions were prepared in duplicates. Each plate contained a set of non-template controls and controls for gDNA contamination. Gene expression was calculated using a modified ΔΔC approach [24].
2.12 In silico analyses
Two independent publicly available datasets (Normal Breast [25] from UCSC Xena functional genomics platform and Breast Invasive Carcinoma from TNMplot.com integrated database) were used to analyse mRNA levels of FGFR2 and ITGB1, as well as profiles of gene expression correlations in low vs. high cancer risk normal breast tissue samples and paired tumour and adjacent normal breast tissues, respectively [26, 25]. Breast cancer risk estimate in UCSC Xena cohort is based on assigned Gail risk scores [27]. Five-year breast cancer risk threshold to distinguish between low and high-risk patients was set at 1.67% (according to [28]).
2.13 Statistical analyses
All data were presented as relative mean or as the percentage change ± standard deviation (for experiments repeated at least three times) and an unpaired t-test was used to compare the differences between two groups (using GraphPad Prism 8.0.1). For RNAseq datasets analyses differences between two groups were presented as median-based log2 fold change (log2FC) and compared using Mann-Whitney U test. The Kendall’s rank correlation coefficients were calculated for correlation analyses. P-values < 0.05 were considered as statistically significant. Data were analysed and visualized using GraphPad Prism 8.0.1.