2.1 Cell line and culture conditions
The human epithelial colorectal adenocarcinoma cell line (Caco-2) was purchased from NCCS, Pune, Maharashtra (India) and maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma-Aldrich, St. Louis, Missouri, USA) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, Missouri, USA), along with 1% antibiotic solution containing penicillin G (100 µg ml− 1), streptomycin (100 µg ml− 1) and amphotericin (3 µg ml− 1). These cells were routinely grown in 25 cm2 tissue culture flask with 37°C in an atmosphere of 5% CO2 with 90% relative humidity. For different experiments, cells were sub-cultured in 6-well plate till confluency. Cells of 20–40 passage numbers were used throughout the experiments.
2.2 Bacterial strains and culture conditions
An indigenous probiotic L. rhamnosus (LR:MTCC-5897) used under present investigation was previously isolated from household curd and characterized for probiotic attributes (Sharma et al. 2014). For this study, bacterial culture was activated in sterile de Man, Rogosa and Sharpe (MRS) broth (Hi-Media, Mumbai, Maharashtra, India) for 18 h under aerobic incubation at 37°C before use. Next day, activated culture was used to harvest bacterial pellets by centrifugation at 2000 х g for 10 min, followed by washing with phosphate buffered saline (PBS, pH-7.4). For in vitro treatments, bacterial pellets were resuspended in antibiotic free DMEM media to obtain 109 colony forming unit (CFU) ml− 1. The number of bacteria was determined by plate counting on MRS agar plates after aerobic incubation at 37°C for 24–48 h. This particular dose of L. rhamnosus was selected on the basis of previous investigation in which this probiotic was found safe in Caco-2 cells upto 24 h and displayed immunomodulatory effects in weanling mice (Bhat et al. 2019,b).
E. coli strain (ATCC:14948) was obtained from National Collection of Dairy Cultures (NCDC), NDRI, Karnal, Haryana (India). The culture was activated in nutrient broth under aerobic conditions for 18 h at 37°C and preceded as above for further work. For various experiments, the desired bacterial count (1х108 CFU ml− 1) was obtained by plate counting on eosin methylene blue (EMB) agar. Thereafter, the bacteria were re-suspended in antibiotic free DMEM media to attain 100:1/well multiplicity of infection. This specific dose of E. coli was selected through preliminary study performed on barrier integrity in intestinal cells (Bhat et al. 2019, a).
2.3 Stimulation of intestinal cells with bacteria
Caco-2 cells with 1х105 cells ml− 1 density were seeded in 6-well plate and after obtaining confluency, cells were treated with L. rhamnosus (1х109 CFU ml− 1) or E. coli (1х108 CFU ml− 1) for 3 h at 37°C in 5% CO2. For further experiments, Caco-2 cells were incubated with probiotic/E. coli under three different challenge modes known as exclusion (Ex: pre-treatment), competition (Com) and displacement (Dis: post-treatment) respectively. In exclusion assay, Caco-2 cells were incubated with probiotic L. rhamnosus for 3 h, then media was removed and cells were washed with PBS followed by 3 h incubation with E. coli containing DMEM medium for inflammatory stimulation. In competition assay, Caco-2 cells were simultaneously incubated with L. rhamnosus and E. coli for 3 h. While, during displacement assay, Caco-2 cells were initially treated with E. coli containing medium which was then removed after 3 h of incubation and cells were washed with PBS. Later, these intestinal cells were incubated with L. rhamnosus for 3 h. In all these experimental assays, Caco-2 cells grown in DMEM media acted as a negative control. All sets of experiments were carried out in triplicate. The treated cells were washed with ice-cold PBS twice and used for RNA extraction and western blotting.
2.4 RNA isolation and relative expression of genes associated with immune response
Total RNA was isolated from Caco-2 cells following Trizol method as described in manufacturer protocol and further used for relative quantification of genes associated with immune response. Purity of the RNA was confirmed by determining O.D. at 260/280 ratio using microplate spectrophotometer (BioTek Instruments, Winooski, Vermont, USA). RNA integrity was confirmed on 1.5% agarose gel through electrophoresis. Total RNA (1 µg) was reverse transcribed to cDNA using a reverse transcription kit (Thermo Fisher Scientific, Waltham, Massachusetts, USA) following user manual. The prepared cDNA was stored in -20°C until used further. Quantitative real-time PCR (qRT) analysis, reactions were conducted to determine the relative gene expression by using ABI-fast 7500 thermocycler system (Applied Biosystems, California, USA). For mRNA expressions, qRT-PCR reactions were performed in 10 µl reaction volume containing 1 µl of test sample, 5 µL of syber (Thermo scientific, USA), 0.5 µl of each primer and 3 µl nuclease free water. Sequences of primers are shown in Table 1. GAPDH was used as a reference gene throughout the experiments. The thermal profile for reaction was: initial denaturation of 5 min at 94°C, 35 cycles of denaturation (94°C for 30 sec), annealing (60°C for 30 sec) and extension (60°C for 45 sec) and final extension cycle at 60°C for 5 min. After amplification, threshold (Ct) values of both control and treatment groups with reference genes (GAPDH) were used for calculating fold changes in respective target genes expression (Livak and Schmittgen 2001).
Table 1
Sequence of primers along with their corresponding amplicon size for mRNA quantification immunity related genes using qRT-PCR
Gene | Sequence of primer | Amplicon Length (bp) | Accession number |
Genes related to Interleukins |
IL-8 | F 5’-GGTGCAGTTTTGCCAAGGAG-3’ R 5’-TTCCTTGGGGTCCAGACAGA-3’ | 183 | NM_001354840.2 |
IL-6 | F 5’-GGCACTGGCAGAAAACAACC-3’ R 5’-GCAAGTCTCCTCATTGAATCC-3’ | 85 | NM_001371096.1 |
TNF-α | F 5’-GGGACCTCTCTCTAATCAGC-3’ R 5’-TCAGCTTGAGGGTTTGCTAC-3’ | 103 | NM_000594.4 |
IL-23 | F 5’-GTGGGACACATGGATCTAAGAGA-3’ R 5’- CTGGTGGATCCTTTGCAAGC-3’ | 135 | NM_016584.3 |
Genes related to pathogen recognition receptor (PRR) |
TLR-2 | F 5’-AGCACTGGACAATGCCACAT-3’ R 5’-ACCATTGCGGTCACAAGACA-3’ | 113 | NM_001318796.2 |
TLR-4 | F 5’-CAAGAACCTGGACCTGAGCTT-3’ R 5’-AAAAGGCTCCCAGGGCTAAA-3’ | 200 | NM_138554.5 |
MyD-88 | F 5’-CAGCGACATCCAGTTTGTGC-3’ R 5’-GGCGGCACCTCTTTTCGAT-3’ | 146 | NM_002468.5 |
Genes related to NF-κB pathway |
NF-κB | F 5’-ATGTGGGACCAGCAAAGGTT-3’ R 5’-CACCATGTCCTTGGGTCCAG-3’ | 134 | NM_001319226.2 |
SIGIRR | F 5’-GGTATGTCAAGTGCCGTCTCAAC-3’ R 5’- AGCTGCGGCTTTAGGATGAAGT-3’ | 120 | NM_001135054.2 |
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2.5 Enzyme linked immunosorbent assay
Cytokines secretions (TNF-α, IL-10, TGF-β and IFN-ϒ) were evaluated by enzyme linked immunosorbent assay (ELISA) (Biolegend Inc., San Diego, California, USA) in supernatants of Caco-2 cells according to manufacturer protocol. In brief, 96-well immune plates (Hi-media, Mumbai, Maharashtra, India) were coated with 100 µl of capture antibody and incubated overnight at 4°C. Next day after PBS/T washing, 200 µl of blocking buffer was added to each well to avoid non-specific binding. Afterward, serially diluted respective standard cytokines or undiluted culture supernatant was used to determine the concentrations of interleukins. Then, 100 µl well− 1 of detection antibody of respective cytokines were added. Later, 100 µl well− 1 HRP-conjugated avidin was added as detection enzyme. In final step, TMB substrate (3,3,5,5-tetramethyl diamine benzidine containing 0.03% H2O2) was added for the development of colour and 2 N H2SO4 was used to stop the reaction. After that plate was read at 450 nm by using a microplate reader (BioTek Instruments, Winooski, Vermont, USA).
2.6 Extraction of protein and determination of NF-κB nuclear translocation by western blotting
Cytoplasmic and nuclear extracts of experimentally treated Caco-2 cells were collected by cell lysis using extraction reagents (Cytoplasmic nuclear extraction reagents Kit, Infobio, India) and protein concentrations were determined using Lowry method (Lowry 1951). After that, protein samples (30 µg well− 1) were separated on SDS-PAGE (Laemmli 1970) followed by blotting on PVDF membrane for detection of a specific protein. This membrane was blocked with 5% BSA (overnight) and incubated with primary antibody for 4 h at room temperature against NF-κB p-65 (1:100 dilution, Santa Cruz Biotech Inc, Dallas, Texas, USA), β-actin (1:1000 dilution, Sigma-Aldrich, St Louis, Missouri, USA) and Lamin (1:500 dilution, Santa Cruz Biotech Inc, Dallas, Texas, USA). The membrane was washed and incubated with horseradish peroxidase conjugated secondary antibody (Sigma-Aldrich, St Louis, Missouri, USA) for 2 h at room temperature. Signals were detected by using Dab Membrane Peroxidase tablets (Genetix, San Jose, California, USA).
2.7 Statistical analysis
Data were analysed using GraphPad Prism (Version 5.01) software. Experimental results are presented as means ± S.E.M. Data were subjected to analysis of variance (ANOVA) and the Tukey test was used to separate the means (p < 0.05) which were considered statistically significant.