Chemicals
All chemicals were purchased from Sigma-Aldrich (St. Louis, MO, USA) unless stated otherwise. The sources of key chemicals are assembled in Table 1. UDCA was purchased from Sigma-Aldrich (St. Louis, MI, USA) and was dissolved in dimethyl sulfoxide (DMSO) to achieve the final concentration of 100 mM. Cisplatin was dissolved in 1xPBS at the concentration of 3 mM, ML385 was dissolved in DMSO in the concentration of 50 mM.
Table 1. The source of key chemicals
Compound
|
Company
|
Ref. No.
|
UDCA
|
Sigma-Aldrich
3050 Spruce Street, Saint Louis, MO 63103, USA
|
U5127
CAS 128-13-2
|
cisplatin
|
Sigma-Aldrich
3050 Spruce Street, Saint Louis, MO 63103, USA
|
232120
CAS 15663-27-1
|
ML385
|
Selleck Chemicals
14408 W Sylvanfield Drive, Houston, TX 77014 USA
|
S8790
CAS 846557-71-9
|
Cell lines
A2780 cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 1% penicillin-streptomycin.
ID8 cells were cultured in high glucose DMEM (4.5 g/L glucose) medium supplemented with 4% fetal calf serum, 2 mM L-glutamine, 1% penicillin-streptomycin, 1% ITS supplement (I3146).
Cisplatin resistant A2780 cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 2 mM glutamine, 1% penicillin-streptomycin. Cisplatin resistant cells underwent selection (1 µM cisplatin) once a week for3 days before plating for assay.
Cell lines were regularly checked for mycoplasma contamination.
Methylthiazolyldiphenyl-tetrazolium bromide (MTT) reduction assay
MTT reduction assay was measured as previously described [33]. The assay determines the activity of mitochondrial complex I and can be used to detect rapid toxicity and the induction of apoptosis [86]. Briefly, cells were plated in 96 well plates the day before the assay. A2780 cells or cisplatin resistant A2780 cells were plated in 96 well plates for MTT assays with a number of 104 cells/well. On the next day, cells were treated with cisplatin in itself or in a combination with 300 nM UDCA for 4 hours. Cisplatin was applied between the concentrations of 100 µM and 0.0017 µM with one-third dilution. Vehicle controls were DMSO for UDCA and 1xPBS for cisplatin.
Sulforhodamine B assay
The SRB assay measures acid-precipitable protein onto cells that is proportional to cell number, hence can be used to assess cell proliferation or long-term cytostasis [87]. SRB proliferation assay was measured as previously described [33].
For Figure 1., A2780 cells (103 cells/well) were plated to 96 well plates and were treated with UDCA on the next day for 48 hours. For concentration range of serum reference, UDCA was applied between 1000 nM and 86 nM with four-fifths dilution. For therapeutic concentration range UDCA was applied between 15 µM and 0.4 µM with two-thirds dilution.
For Figure 2., A2780 cells (2x103 cells/well) and cisplatin resistant A2780 cells (6x103 cells/well) were plated in 96 well plates. On the next day, cells were treated with cisplatin in itself or in a combination with 300 nM UDCA for 48 hours. Cisplatin was applied between the concentrations of 100 µM and 0.0017 µM with one-third dilution. Vehicle controls were DMSO for UDCA and 1xPBS for cisplatin.
Impedance measurements
Electric cell-substrate impedance sensing (ECIS Z-Theta, Applied BioPhysics) was applied as described previously [88]. A2780 cells (2x104 or 5x104) were plated into 8W10E ECIS plates (3-4 well/condition). This plate is recommended to monitor cell-cell connections. Impedance measurement was initiated upon plating and was continued onwards. Impedance was measured at multiple frequencies between 62.5 Hz and 64 kHz in 120 or 150 seconds (as a function of cell numbers) time intervals in real time. After reaching confluency (plateau in capacitance and resistance), half of the medium was replaced by 600 nM UDCA (yielding a final concentration of 300 nM) or DMSO as vehicle control. The impedance value corresponding to the plateau (i.e. confluence) was regarded as a baseline value. Impedance measurement was resumed for 24 hours. The average of the resistance values at 4 kHz ±30 minutes before and after the peak resistance was regarded as a peak value. The difference between the peak and the baseline values were expressed as fold change compared to the DMSO-treated samples and were plotted. All plates contained a well containing only medium as a background control for background correction.
Western blot
Cells were lysed in RIPA buffer (50 mM Tris, 150 mM NaCl, 0.1% SDS, 1% TritonX 100, 0.5% sodium deoxycolate, 1 mM EDTA, 1 mM Na3VO4, 1 mM NaF, 1 mM PMSF, protease inhibitor coctail). Protein concentrations were determined using a BCA protein assay kit (Pierce Biotechnologies, Rockford, IL, USA). Protein extracts were loaded onto 10% SDS polyacrylamide gels. After electrophoresis, proteins were transferred to nitrocellulose membranes and blocked using 5% BSA for 1 h at room temperature. Then, membranes were incubated with primary antibodies for overnight at 4 °C. Membranes were washed with Tris-buffered saline containing 0.1% Tween (TBS-T) followed by a 1 h incubation with IgG HRP conjugated secondary antibody (Cell Signaling Technology, Inc. Beverly, MA, 1:2000). Membranes were washed with TBS-T and visualization was performed by SuperSignal West Pico Solutions (Thermo Fisher Scientific). b-actin was used as a loading control. Blots were quantified by densitometry using Image Lab 6.1 software.
Antibodies used in this study are listed in Table 2.
Table 2. The antibodies used in the study
Abbreviations: mAb – monoclonal antibody, pAb – polyclonal antibody
Name
|
Species
|
Ig class
|
Dilution
|
Vendor and Cat No.
|
RRID
|
|
|
Actin
|
Rabbit pAb
|
|
1:30000
|
Sigma-Aldrich
A2066
|
AB 476693
|
|
Akt
|
Rabbit pAb
|
|
1:1000
|
Cell Signaling Technology
#9272
|
AB 329827
|
|
Phospho-Akt (Ser473) (D9E) XP®
|
Rabbit mAb
|
IgG
|
1:2000
|
Cell Signaling Technology
#4060
|
AB 2315049
|
|
AMPKα (D63G4)
|
Rabbit mAb
|
|
1:1000
|
Cell Signaling Technology
#5832
|
AB 10624867
|
|
Phospho-AMPKα (Thr172) (40H9)
|
Rabbit mAb
|
IgG
|
1:1000
|
Cell Signaling Technology
#2535
|
AB 331250
|
|
KEAP1 (D6B12)
|
Rabbit mAb
|
IgG
|
1:1000
|
Cell Signaling Technology
#8047
|
AB 10860776
|
|
Nrf2
|
Rabbit pAb
|
IgG
|
1:1000
|
Abcam
ab31163
|
AB 881705
|
|
Nrf2
|
Rabbit pAb
|
IgG
|
1:1000
|
Novus Biologicals NBP1-32822
|
AB 10003994
|
|
p70 S6 Kinase (49D7)
|
Rabbit mAb
|
IgG
|
1:1000
|
Cell Signaling Technology
#2708
|
AB_390722
|
|
Phospho-p70 S6 Kinase (Thr389)
|
Rabbit pAb
|
|
1:1000
|
Cell Signaling Technology #9205
|
AB 330944
|
|
Snail (C15D3)
|
Rabbit mAb
|
IgG
|
1:1000
|
Cell Signaling Technology #3879
|
AB 2255011
|
|
4 Hydroxynonenal
|
Rabbit pAb
|
IgG
|
1:1000
|
Abcam
ab46545
|
AB_722490
|
|
β-Catenin (D10A8) XP®
|
Rabbit mAb
|
IgG
|
1:1000
|
Cell Signaling Technology #8480
|
AB_11127855
|
|
Anti-rabbit IgG HRP-linked
|
Goat
|
IgG
|
1:10000
|
Cell Signaling Technology #7074
|
AB_2099233
|
|
Total RNA preparation and reverse transcription-coupled quantitative PCR (RT-qPCR)
Total RNA from A2780 cells was prepared using TRIzol reagent (cat. no. TR118, Molecular Research Center Inc., Cincinnati, OH, USA) according to the manufacturer’s instructions. DNase treatment of total RNA samples was performed using 2U of DNaseI (cat. no. AM2222, Thermo Fisher Scientific) per 10 µg RNA. Two μg of total RNA were used for reverse transcription using High-Capacity cDNA Reverse Transcription Kit (cat. no. 4368813, Thermo Fisher Scientific) according to the manufacturer’s instructions. The reverse transcription reaction mixtures were supplemented with RNase inhibitor (cat. no. N8080119, Thermo Fisher Scientific). The cDNA was cleaned with the nucleospin Gel and PCR clean-up (Macherey-Nagel Gmbh & Co. KG, Düren, Germany) according to the manufacturer’s instructions.
The qPCR reactions were performed with qPCRBIO SyGreen Lo-ROX Supermix (PCR Biosystems Ltd., London, UK) using 20 ng diluted cDNA with the appropriate primers at 500 nM final concentration in 10 μl total volume. Amplification reactions were performed using a Light-Cycler 480 system (Roche Applied Science, Basel, Switzerland). Cycling conditions are given in Table 3. Primers are listed in Table 4.
Table 3. Cycling conditions of qPCR reactions
Step
|
Temperature
|
Time
|
Cycles
|
Polymerase activation
|
95°C
|
10 min
|
1
|
Denaturation
|
95°C
|
10 s
|
50
|
Annealing/Extension
|
62°C
|
20 s
|
Melting curve analysis
|
95°C
|
5 s
|
1
|
65°C
|
1 min
|
65°C to 97°C (Continuous)
|
ramp rate 0.11°C/s
|
40°C
|
30 s
|
Table 4 The specifics of the primer sets used in the study
Reporting is made in accordance with the QIME guideline [89, 90]
Gene name
|
Primers (5’-3’)
|
Length (bp)
|
Specificity check
|
Alignments (Sequence ID)
Query coverage 100%
Percent identity 100%
|
Primer location
|
Exon intron boundary
|
Calibration curve
|
Efficiency
|
NRF2
|
FW:
TGAGCAAGTTTGGGAGGAGCT
REV: ACTGGTTGGGGTCTTCTGTGG
|
245
|
BLAST
|
NM_001313903.2
|
FW 484-504
REV 728-708
|
YES
|
Slope: -3.428
YIntercept: 28.11
Error=0.0735
|
1.958
|
NM_001313902.2
|
FW 613-633
REV 857-837
|
NM_006164.5
|
FW 703-723
REV 947-927
|
NM_001313904.1
|
FW 1165-1185
REV 1409-1389
|
NM_001313901.1
|
FW 1202-1222
REV 1446-1426
|
NM_001313900.1
|
FW 1110-1130
REV 1354-1334
|
NM_001145413.3
|
FW 1215-1235
REV 1459-1439
|
NM_001145412.3
|
FW 1236-1256
REV 1480-1460
|
TCF7L2
|
FW:
ACGTACAGCAATGAACACTTCAC
REV:
GGCGATAGTGGGTAATACGG
|
128
|
BLAST
|
NM_001198530.2
|
FW 952-974
REV 1079-1060
|
YES
|
Slope: -3.699
YIntercept: 29.42
Error = 0.204
|
1.863
|
NM_001146283.2
|
FW 1195-1217
REV 1322-1303
|
NM_001349870.2
|
FW 778-800
REV 905-886
|
NM_001146285.2
NM_001198528.2
NM_001146286.2
NM_001198527.2
NM_001198526.2
NM_001146284.2
NM_001198525.2
NM_001198529.2
NM_030756.5
|
FW 1054-1076
REV 1181-1162
|
NM_001367943.1
NM_001146274.2
NM_001363501.2
NM_001198531.2
|
FW 1123-1145
REV 1250-1231
|
NM_001349871.1
|
FW 310-332
REV 437-418
|
PPIA
|
FW:
GTCTCCTTTGAGCTGTTTGCAGAC
REV:
CTTGCCACCAGTGCCATTATG
|
171
|
BLAST
|
NM_021130.5
|
FW 102-125
REV 272-252
|
YES
|
Slope: -3,485
YIntercept: 25.54
Error= 0.0366
|
1.936
|
RPLP0
|
FW:
CCATTGAAATCCTGAGTGATGTG
REV:
GTCGAACACCTGCTGGATGAC
|
131
|
BLAST
|
NM_053275.4
|
FW 589-611
REV 719-699
|
YES
|
Slope: -3.552
YIntercept: 30.65
Error= 0.0548
|
1.912
|
NM_001002.4
|
FW 529-551
REV 659-639
|
Boyden chamber experiments
Cell invasion assay was determined using Corning BioCoat Matrigel Invasion Chambers (Corning, NY, USA) with 8.0 µm PET membrane in 24-well plates (cat.no.# 354480). In the control setup similar 8 µm PET membranes were used that were devoid of the matrigel layers. Cells (20.000 cells/well) were added to the top of insert in upper chamber in serum free medium and were seeded overnight. Then, cells were treated with LCA (0.03 µM) in 0.5 ml serum free medium. Simultaneously medium (0.75 ml) containing 10 % FBS, LCA (0.03 µM) and 100 ng/ml stromal cell-derived factor 1α (SDF1α) (Sigma-Aldrich, cat.no.# SRP4388) was added to the lower chamber as chemoattractant. After 48 h, non-invaded cells on the top of the filters were wiped off with cotton swabs. The lower surface of membranes containing invaded cells were washed in PBS and fixed with 100% methanol and stained with DAPI. The invading cells were counted with Opera Phoenix High Content Screening System (Perkin-Elmer Waltham, MA, USA) and pictures were analyzed using the Harmony 4.6 Software. The following calculations were performed:
% Invasion = (Mean of cells invading through Matrigel insert membrane / Mean of cells invading through Control insert membrane) *100
Invasion index = % Invasion of the Treated cell / % Invasion of the Control (non-treated) cell
Seahorse measurements
A2780 (6x103) or ID8 (5x103) cells were plated into Seahorse XF96 cell culture microplates (Agilent Technologies, Inc., Santa Clara, CAL, USA) and were treated with 300 nM UDCA or DMSO (as vehicle). In a subset of experiments UDCA-treated cells were treated with ML385 (1µM) for 48 hours. At the end of treatment medium was replaced by buffer-free DMEM supplemented with glucose (1 g/L) and the plate was incubated in a CO2-free incubator for at least 1 hour and then the plate was subjected to Seahorse measurement using the Seahorse XF96 instrument. Five minute measurements were made that was repeated 5 times, interspersed by 30 seconds of mixing. After the assay cell numbers were determined by SRB assay. The stable ECAR readouts were averaged for each well, the first measurement point was omitted. The ECAR values were normalized for the SRB absorbance.
Database screening
We assessed the survival data in GEPIA2 [91] and database.
Statistical analysis
Statistical analysis was performed using 8.0.1 version of Graphpad Prism. Values were tested for normal distribution using the test indicated in the figure legends. When necessary, values were log normalized. The following statistical test, post hoc test and the level of significance is indicated in the figure captions. Nonlinear regression was performed using the built-in “[Inhibitor] vs. response – Variable slope (four parameters), least square fit” utility of Graphpad that yielded IC50 and Hill slope values.