Cell culture:
The human BrCa cell lines MDA-MB-231, MCF7, and MDA-MB-453 were procured from the American Type Culture Collection (ATCC), Manassas, VA, USA, and PCa cell line LNCaP was purchased from the National Centre for Cell Science, Pune, Maharashtra, India. MDA-MB-231 and MDA-MB-453 were cultured in Leibovitz's L-15 Medium, MCF7 in Minimum Essential Medium Eagle (MEM) along with 0.01 mg/ml human recombinant insulin, and LNCaP cells in RPMI-1640 media (Catalog: AL120A, HiMedia). The culture media was supplemented with Fetal Bovine Serum to a final concentration of 10% and 1% Antibiotic Antimycotic Solution (v/v). The culture media and associated components were purchased from HiMedia Laboratories, Mumbai, India. The cell lines were maintained in an incubator with normoxic conditions, as per ATCC recommendations. The representative images of breast cancer cells and their receptor status is attached in Figure S1.
AR antagonists’ treatment:
For treatment of Bicalutamide (14250, Cayman Chemical, MI, USA) and Enzalutamide (11596, Cayman), the three breast cancer cell lines were seeded into 90 mm Petri dishes. At ~60% confluence, the culture media was replenished with phenol red-free RPMI-1640 media (Catalog: AT120, HiMedia) supplemented with charcoal-stripped FBS (Catalog: RM10416, HiMedia). At ~75% confluence, cells were treated with Bicalutamide and Enzalutamide at 1 µM concentration. 24 hours post-stimulation, cells were harvested to extract RNA and protein for further experiments. The experiments were conducted independently in three biological replicates.
Clinical study design and assessments:
This was a cross-sectional study conducted in the Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), New Delhi, in a closed collaboration with the departments of Surgical Disciplines, Surgical Oncology, and Pathology, AIIMS, New Delhi. The ethics committee approved this study from an ethical perspective for postgraduate research of AIIMS, New Delhi, vide Ref. No. IECPG-177/27.03.2019, RT-08/22.04.2019 dated April 29, 2019.
Enrollment of Patients and baseline data collection:
Participants were identified from a cohort of primary breast cancer patients undergoing surgical intervention for de novo breast carcinoma at the AIIMS, New Delhi, a tertiary healthcare center in Northern India. Informed consent from participants was obtained from the subjects prior to the recruitment into the study. All the participants were of Indian origin and 18+ years of age. We reviewed the demographic and clinical data (age, menopausal status, localization, BI-RADS score, tumor size (pathological), lymph node involvement, ER, PR, HER2 status, Ki67 scores, and histological grades from the hospital patient record for clinical correlation. Patients were followed up primarily through outpatient department services or with hospital records for survival assessment.
Processing of Patient’s tissue samples:
The tumor core and adjacent benign tissue were collected in RNA later solutions (AM7021, Invitrogen) from the recruited subjects post-operatively. The Tumor specimens were processed for subsequent RNA and whole-cell lysate isolation. The matched tissues were formalin-fixed, paraffin-embedded (FFPE) for routine histopathological examination. These FFPE blocks were used for immunohistochemical evaluations of AR and AR-V7 after sectioning (5 µm) and adherence to poly-L-lysine-coated glass slides.
RNA extraction and cDNA synthesis:
RNA was isolated from cell lines and tissue specimens using ReliaPrep RNA Miniprep Systems (Z6011, Promega) according to the manufacturer's directions. The samples were treated with deoxyribonuclease to rule out any DNA contamination. Complementary DNA was reverse transcribed from total RNA (2 μg) using random hexamers following Verso cDNA Synthesis Kit (AB1453A, Thermo Scientific) protocol.
Reverse transcription-quantitative PCR analysis:
Real-time quantitative PCR was performed on AriaMx Real-time PCR system (G8830A, Agilent) using DyNAmo ColorFlash SYBR Green qPCR Kit (F416L, Thermo Scientific) according to the manufacturer's instructions. Primers were designed specifically for AR-targeting all transcript variants, AR-FL, and AR-V7 only. The primers used are listed in Table 4 in the supplementary information. PCR cycling conditions consisted of an initial denaturation step (7 minutes at 95°C) and 40 cycles of PCR (10 seconds at 95°C, 20 seconds at 60°C, and 20 seconds at 72°C). All qRT-PCR assays were conducted in two technical replicates and three biological replicates. Gene expression analysis was performed using Vandesompele et al., which offers a normalization strategy that uses multiple reference genes and takes primer efficiency into account.[26]
Western blot analysis:
Cells and tissue specimens (followed by crushing and sonication) were lysed in RIPA lysis buffer (50 mM Tris HCl, 150 mM NaCl, 0.1% SDS, 0.5% Sodium deoxycholate, and 1% Triton X) supplemented with protease and phosphatase inhibitor cocktails (#786-108 and #786-782, G Biosciences). The concentration of extracted protein was determined by bicinchoninic acid assay. Protein extracts (40 μg) were separated on 10% sodium dodecyl sulfate-polyacrylamide gels (SDS-PAGE) and electrotransferred onto a Nitrocellulose membrane. Membranes were blocked, and antibodies were diluted in 5% skimmed milk (#GRM1254, HiMedia) followed by overnight incubation with primary antibodies at 4°C and subsequent secondary antibodies incubation for 2 hours at room temperature. The primary antibody used for AR and AR-V7 western blotting was anti-AR mAb (MA5-16412, Invitrogen 1:1000). The secondary antibody used was horseradish peroxidase-tagged anti-rabbit IgG. Immunodetection was performed as per the manufacturer's procedure using an enhanced chemiluminescence reagent (34580, ThermoFisher, Scientific). Blots were stripped off and reprobed with a rabbit polyclonal GAPDH antibody (ITT5052, G-Biosciences 1: 1500) as loading control and normalization. AR immunoblots were quantified using the ImageJ software package (NIH, USA) for densitometric analysis. The western blotting densitometry data was normalized to control tissues and reference protein (GAPDH).
Immunohistochemistry:
Immunohistochemical analysis was performed on tissue specimens against AR-FL and AR-V7 using anti-AR mAb (ab227678, Abcam 1:400) and anti-AR-V7 mAb (ab198394, Abcam 1:200). Tissue slices were deparaffinized using xylene. Antigen retrieval was attained by microwaving slides in citrate buffer (pH 6.0) / Tris-EDTA buffer (pH 9.0) for 30 minutes, followed by endogenous peroxidase blocking using 3% H2O2. Slides were incubated overnight at 4°C with respective antibodies. The staining was visualized using the 3, 3-diaminobenzidine, and hematoxylin as a counterstain. Pathologic evaluation and semi-quantitative scoring were performed by an expert breast cancer pathologist blinded to clinical data. Tumors observed with nuclear staining of 1% or more with intensities of 1+ to 3+ were deemed positive for AR or AR-V7, consistent with previous studies.[27,28]
Statistical analyses:
Statistical analyses were conducted using GraphPad Prism 9.5 and Stata for clinical statistics. The cell lines-based data were parametric and expressed as the mean values and SD derived from three biological replicates. The clinical data in this study were non-parametrically distributed and expressed in median and all individual values. The comparison among different groups was performed using the Mann-Whitney U-test. Any group of outliers were identified using Rout’s method (Q = 1%) and were removed from the study.
Kaplan-Meier analysis was employed to delineate the survival outcomes within the cohort. Survival data were censored up to May 07, 2024. The Hazard Ratio (logrank) was utilized to evaluate the magnitude of influence of AR or AR-V7 expression on survival outcomes. Statistical significance was determined through the log-rank (Mantel-Cox) test. For clinicopathological correlation, univariate analysis was executed with Fisher's exact test (if n = ≤4) and Pearson’s chi-square test (if n ≥5) tests. The p-value of ≤0.05 was considered statistically significant.