Cell culture and treatments
Human 21NT breast cancer cells were cultured in 1x Modified Eagle’s medium alpha (alpha MEM) (Gibco), 2.8 µM hydrocortisone, 1 µg/ml insulin, 10% foetal calf serum (FCS), 1% gluta- max, 10 mM HEPES, 0.1 mM NEAA and 12.5 ng/ml Epithelial Growth Factor (EGF). BT474 cells and PC3 cells were cultured in DMEM F-12 medium (Gibco, Invitrogen) with 10% FBS (Gibco, Invitrogen) and 1% Penicillin-Streptomycin (Gibco). U2OS cells were cultured in McCoy's 5A with 10% FCS (Gibco, Invitrogen) and 1% glutamax, 0.5 µg/ml hydrocortisone. IBR.3 cells were cultured in RPMI 1640 medium (Biosera) with 10% FBS (Gibco, Invitrogen) and 1% Penicillin-Streptomycin (Gibco). HMEC cells were cultured in Basal medium (Mammary Life ™) containing rh Insulin, L-Glutamine, Epinephrine, Apo-Transferrin, rh-TGF, Extract-P, and Hydrocortisone.
Epitalon was purchased from UK Peptides and we were gifted a free sample from Peptides of London. Stock solutions were prepared by dissolving 10 mg of Epitalon in 4 ml of bacteriostatic water, resulting in a concentration of 2.5 mg/ml. Both peptides are certified 99% pure and are compatible with sterile cell culturing. Breast cancer cells (21NT and BT474) were treated daily with (0.1, 0.2, 0.5, and 1.0 µg/mL) of Epitalon for 4 days. Normal fibroblast cells (IBR.3) and epithelial cells (HMEC) were treated daily with 1.0 µg/mL of Epitalon for 3 weeks. Untreated cells were included to serve as a baseline control. Throughout both treatments, the cells were regularly monitored, and the culture media were refreshed daily.
DNA extraction and telomere length measured by qPCR
DNA from human cell lines (21NT, BT474, IBR.3, and HMEC) was isolated using the Wizard genomic DNA purification kit and protocol from Promega (A1120). Telomere length estimation was performed using the qPCR technique (Al-dulaimi et al 2024). A telomeric standard curve was established by serial dilutions of the telomere standard (1018400 kb through 10184 kb dilution) (Table 1). A single-copy gene, 36B4, was used as a genomic DNA control, a serial dilution of the 46B3 standard (6125000 kb through 6.125 kb dilution) was performed. The copy number values generated from the qPCR and the standard curve serial dilutions were used to calculate the total telomere length in kb. (As described by O’Callaghan and Fenech et al 2011).
RNA extraction, cDNA conversion, and qPCR
RNA from 21NT, BT474, IBR.3, and HMEC was extracted, and mRNA gene expression analysis was performed (primers listed in Table 1) using qPCR as described previously (Al-dulaimi et al 2024).
Table 1
Oligomer / gene name | Oligomer sequence | Product size |
|---|
36B4 standard | CAGCAAGTGGGAAGGTGTAATCCGTCTCCACAGACAAGGCCAGGACTCGTTTGTACCCGTTGATGATAGAATGGG | 75 |
Telomere standard | (TTAGGG)14 | 84 |
Telo (F) | CGGTTTGTTTGGGTTTGGGTTTGGGTTTGGGTTTGGGTT | > 76 |
Telo (R) | GGCTTGCCTTACCCTTACCCTTACCCTTACCCTTACCCT | > 76 |
36B4 (F) | CAGCAAGTGGGAAGGTGTAATCC | 75 |
36B4 (R) | CCCATTCTATCATCAACGGGTACAA | 75 |
hTERT(F) | CGGAAGAGTGTCTGGAGCAA | 200 |
hTERT(R) | GGATGAAGCGGAGTCTGGA | 200 |
GAPDH(F) | GAAGGTGAAGGTCGGAGT | 226 |
GAPDH(R) | GAAGATGGTGATGGGATTTC | 226 |
Telomerase Substrate (TS) | AATCCGTCGAGCAGAGTT | |
Anchored Return Primer(ACX) | GCGCGG(CTTACC)3CTAACC | |
Telomerase activity measured by Telomere Repeat Amplification Protocol (TRAP)
The TRAP assay was used to determine telomerase activity. Protein from the 21NT, BT474, HMEC and IBR.3 cells were extracted using the TRAPeze 1 x CHAPS lysis buffer (S7705, Millipore) and quantified using the CB-X protein assay kit (G-Bioscience). For estimation of the telomerase activity, the procedure outlined in (Al-dulaimi et al 2024) was followed. A serial dilution of proteins from 500 ng – 50 ng from the PC3 cell line (telomerase-positive prostate cancer cell) was used to construct a standard curve of telomerase activity. A negative control was also included for enzyme activity by heating 200 ng of the PC3 protein to 95◦C/10 minutes to inactivate the telomerase enzyme. For each qPCR reaction, 25 µl of master mix was prepared by adding 12.5 µl of the 2x Universal SYBR (ThermoFisher) 5.5 µl of RNAse-free water, 1 µl ACX primer (0.05 µg /ul), 1 µl TS primer (0.1 µg /µl) (Table 1), and 4 µl of the protein sample. The reactions were incubated at 25◦C for 20 min to allow telomerase to synthesise the TRAP ladders, then the qPCR was carried out at 95◦C for 10 min and 35 cycles of 95◦C for 30 s, and 60◦C for 90 s. Telomerase activity was quantified using the PC-3 hTERT standard curve and QuantStudio V1.3 software.
ALT activity quantified using the C-circle assay
C-circle assay was performed as previously described (Al-dulaimi et al 2024). 30g of genomic DNA was diluted in 10 mM TRIS (pH 7.6) buffer. The diluted genomic DNA was added to a 10 µl reaction mix containing 0.2 mg/ml BSA, 4 mM DTT, 0.10% Tween, 0.1 mM dTTP, 1X phi29 buffer, and 15 U phi 29 DNA polymerase. Reactions without the phi 29 polymerase enzyme were included as a negative control. Samples were incubated for 8 h at 30◦C followed by 65◦C for 20 min. The levels of telomeric DNA in samples were quantified using qPCR, the reference gene used was the single-copy gene 36B4, with primers for both telomeric and 36B4 sequences outlined in Table 1. The qPCR cycling conditions were as follows: an initial denaturation at 95°C for 15 minutes, followed by 30 cycles of 95°C for 7 seconds and 58°C for 10 seconds, and a final extension step at 95°C for 5 minutes, then 40 cycles of 95°C for 15 seconds and 58°C for 30 seconds. The C-circle assay was performed using qPCR QuantStudio V1.3 software. Standard curves for the telomere standard and reference gene were used to calculate telomere lengths in kilobases.
Immunofluorescence for PML bodies
21NT cells (treated with 1ug/ul epitalon and untreated) were plated onto glass microscope slides (Thermo Scientific), then fixed in 2% formaldehyde (Fisher Scientific) for 15 min and cold methanol for 10 min. Following this, they were washed with PBS and permeabilized with 0.3% (v/v) Triton X-100 (Sigma-Aldrich) solution for 5 min. Cells were washed with PBS and blocked with 5% BSA for 1 h at RT. Cells were then incubated with a mouse monoclonal primary antibody against PML (PG-M3): sc-966) diluted in blocking solution for 2 h at RT. Following this, they were washed three times with PBST (1X PBS and 0.05% Tween-20), then incubated with mouse IgG FITC conjugated secondary antibody (Invitrogen). After a one-hour incubation, the cells were washed three times with PBST and stained with DAPI. For each slide, 100 cells were counted using Lecia microscope with a 100 X objective to confirm the presence of PML bodies.
Statistical analysis
All statistical analyses were carried out using GraphPad Prism (GraphPad Software). Statistical analysis was performed using unpaired Student’s test (*P < 0.05 **P < 0.01, ***P < 0.001). Three biological repeats under the same conditions were performed for all experiments.