Public database
Two cohorts of 1108 and 379 patients with breast cancer (TCGA, Firehose legacy; The Metastatic Breast Cancer Project, Provisional, December 2021) were investigated from the cBioportal database (https://www.cbioportal.org/, assessed on November 18th, 2022) [19, 20]. Messenger RNA values were determined using RNA-Seq by Expectation-Maximization (RSEM) on a log-2 scale. Pearson’s correlation analyses were separately performed in these two cohorts of 960 and 157 patients, who had complete information both for L1CAM and FOXC1. Furthermore, in the TCGA cohort, L1CAM transcription was compared between high (n = 375) or low (n = 585) FOXC1 transcription groups, which were determined using the mean as the cutoff.
Cell Culture And Specimens
Four human TNBC cell lines SUM149, HCC1937, MDA-MB-231 and BT549, were obtained from the ATCC (American Type Culture Collection, Manassas, VA, USA). Cells were cultured in RPMI1640 (Gibco, ThermoFisher, Waltham, USA) supplemented with 10% fetal bovine serum (FBS, Biological Industry, Kibbutz BeitHaEmek, Israel).
Transient Transfection
Twenty-four hours prior to transfection, approximately 2×105 cells (BT549, MDA-MB-231, or HCC1937) were seeded into 6-well plates and allowed to reach 80–90% confluence by the second day. To knock down L1CAM, BT549 cells were transiently transfected with L1CAM siRNA (BT549-siL1CAM) or control scramble siRNA (BT549-siNC) using Lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. The siRNA targeting L1CAM and the control scramble siRNA were purchased from HIPPOBIO (Shenzhen, China), with the following sequences: si-L1CAM: forward: 5′-GAACGGCAACCUCUACUUUTT-3′ and reverse: 5′-AAAGUAGAGGUUGCCGUUCTT-3′; siNC: 5′-UUCUCCGAACGUGUCACGUTT-3′ and reverse: 5’-ACGUGACACGUUCGGAGAATT-3’. To deplete FOXC1, BT549 cells were transfected with the shRNA of FOXC1 (BT549-shFOXC1) or scrambled sequence as a control (BT549-shNC), that were cloned into the pLV-hU6-Neongreen construct (SyngenTech, Beijing, China). Cells with stably decreased FOXC1 were then selected with 1 µg/mL puromycin. Furthermore, to overexpress L1CAM, BT549-shFOXC1, MDA-MB-231 and HCC1937 cells were transfected with a full length human L1CAM mRNA (NM_000425), that was inserted into the GV358Vector (GeneChem, Shanghai, China) and were selected with 400 µg/mL, 1mg/mL and 1mg/mL Geneticin (BT549-shFOXC1-L1CAM, MDA-MB-231-L1CAM and HCC1937-L1CAM), respectively.
Wound Healing Assay
BT549-shFOXC1, BT549-siL1CAM, BT549-shFOXC1-L1CAM, MDA-MB-231-L1CAM and HCC1937-L1CAM and their respective control cells were seeded at a density of 5 × 105 cells per well in 6-well plates. The monolayer of cells was scratched with a 1 mL plastic pipette tip to create a uniform wound. After 24 hours of incubation, the wound width was then examined under a phase-contrast microscope (NIKON; Konan, Tokyo, Japan). Photographs of at least 3 random fields were taken, and in each filed, the closure of the gap distance was calculated at 0 and 24 hours. Cell migration percentages (%) were calculated using the following formula: [(0-hour-gap distance − 24-hour-gap distance) / 0-hour-gap distance] × 100. All distances were measured by ImageJ software.
Migration And Invasion Assays
Transwell chambers (Corning, NY, USA) were used to detect cell migration and invasion. The bottom of the transwell chamber was made of a polycarbonate membrane with 8 µm pore diameter. For invasion assays, an additional Matrigel (50 µl BD biosciences, Franklin Lakes, NewJersey, US) was used to coat the surface of the polycarbonate membrane. For each cell line, 5×104 cells were suspended in 200 µl serum-free RPMI1640 medium, and seeded into the upper chamber, and 600 µl 10% FBS-supplemented RPMI1640 medium was added to the lower chamber. After 24 hours, the upper chamber and cells on the upper surface of the membrane were removed. Cells that had migrated to the lower surface of the membrane were stained with 0.1% crystal violet, and the number of cells was counted under a Leica microscope under 100× magnification (DM3000, Wetzlar, Germany). Four fields from each sample were randomly selected for counting cells. Results were summarized by the average of three replicates, and each experiment was repeated three times.
Cell Proliferation Assay
To measure cell viability, cells were separately seeded into 96-well plates at a concentration of 2000 cells per well; then after four to five hours, cells were first incubated with 20 µl CCK-8 solution (C0038, Beyotime Biotechnology, China) for 2.5 hours in a humidified chamber at 37℃, and then absorbance was detected (OD value: optical density) at a wavelength of 450 nm using a microplate reader (Multiskan MK3, ThermoFisher, CA, US). Results were summarized by four technical replicates, and each experiment was repeated for triple times.
Real-time Polymerase Chain Reaction
Total RNAs were extracted from cells using TRIzol (cat#15596026) and reverse transcription of purified RNAs was performed using oligo (dT) priming and Superscript III reverse transcriptase according to the manufacturer’s instructions (TaKaRa, Tokyo, Japan). Real-time PCR was performed using a SYBR Premix kit (TaKaRa, Tokyo, Japan). β-Actin was used as a loading control. The reactions were undertaken with a 7300 Real-Time PCR System (Applied Biosystems, Waltham, MA, USA). The primer pairs used for target genes were purchased from SangonBiotech (Shanghai, China) as follows:
FOXC1 forward, 5′-TCACAGAGGATCGGCTTGAAC-3′,
FOXC1 reverse, 5′-TCCTGCTTTGGGGTTCGATT-3′,
L1CAM forward, 5′-CCCCGAGGAATTGATGGAGC-3′,
L1CAM reverse, 5′-GGTTCTGGTAGGTGACACGG-3′,
β-actin forward, 5′-CATGTACGTTGCTATCCAGGC-3′,
β-actin reverse, 5′-CTCCTTAATGTCACGCACGAT-3′.
Western Blot Analysis
Cells were first lysed with a cell lysis buffer containing phenylmethylsulfonyl fluoride (Beyotime, Shanghai, China). Proteins (30 µg) of each cell lysate were then separated by SDS-PAGE and transferred onto a polyvinylidene difluoride (PVDF, Millipore, Bedford, MA, USA) membrane followed by blocking with bovine serum albumin, and incubating at 4℃ overnight with primary antibodies anti-FOXC1 (1:500, ab223850; Abcam, Cambridge, UK), anti-L1CAM (1:1000, ab270455; Abcam, Cambridge, UK), anti-GAPDH (1:2000, sc-47724; Santa Cruz Biotechnology, Dallas, TX, USA), and anti-β-tubulin (1:3000, sc-5274; Santa Cruz Biotechnology, Dallas, TX, USA) in blocking buffer. Following washes with TBST (Tris-buffered saline with 0.2% Tween20), the blots were incubated with horseradish peroxidase-labelled anti-rabbit (1:10000, ab205718; Abcam, Cambridge, UK) or anti-mouse (1:5000, ab6728; Abcam, Cambridge, UK) at room temperature for two hours, washed with TBST, followed by signal detection using chemiluminescence. Protein bands were visualized using an ECL western blotting substrate (cat#32109, ThermoFisher, USA).
Patients And Tumor Specimens
Paraffin-embedded archival pathological specimens from 44 patients diagnosed with TNBC were available, along with complete clinicopathological features. The patients had undergone biopsy without preoperative therapy at the Cancer Hospital of Shantou University Medical College between January 2013 and December 2019. Of this cohort, most of patients (n = 34) were diagnosed with early stages (I/II), while the rest were at the advanced stages (III/IV) except for one with unknown stage. Clinical tumor stage (TNM stage) was grouped in accordance with the American Joint Committee on Cancer, 6th Edition Cancer Staging Manual (2002). Participants gave their informed consent after being notified of the details and potential consequences. This study of tumor samples was approved by the medical ethics committee of the Cancer Hospital of Shantou University Medical College (approval number: 2019024).
Immunohistochemistry
Immunohistochemistry (IHC) for detecting FOXC1 and L1CAM in TNBC was carried out. Briefly, sections (4-µm thick) were fixed in 10% buffered formalin and embedded in paraffin. After deparaffinization and rehydration, endogenous peroxidase activity was blocked with 0.3% hydrogen peroxide for 30 minutes. Then tissue sections were autoclaved at 121°C in citrate buffer (pH 6.0) for 10 minutes, and incubated with rabbit anti-FOXC1 monoclonal antibody (1:50, ab223850; Abcam, Cambridge, UK) or L1CAM antibody (1:100, ab270455; Abcam, Cambridge, UK). IHC staining was carried out with an EnVision antibody complex (anti-mouse/rabbit) method using an ElivisionTM plus Polymer HP (Mouse/Rabbit) IHC Kit (MXB Biotechnologies, Fujian, China) and 3,3’-diaminobenzidine as the chromogen substrate. IHC staining for FOXC1 and L1CAM were scored, by a combination of intensity (0, no staining; 1, weak staining; 2, moderate staining; 3, strong staining) and proportion (0, < 5% of tumor cells stained; 1, 5–25% positive cells; 2, 26–50% positive cells; 3, 51–75% positive cells; 4, more than 76% positive cells). If the product of multiplication between staining intensity and the proportion of positive cells was > 4, expression was defined as positive. Two pathologists independently assessed the cellular location and intensity of immunostaining in each section.
Statistical Analyses
Statistical analyses were performed using GraphPad Prism 8.0 software (San Diego, CA). Data are expressed as mean ± standard deviation (SD). Comparisons of transcriptional levels, cell viability and cell mobility between constructed cells and their controls were conducted using t-tests. For all tests, a value of P < 0.05 was considered significant.