IJO International Journal of Oncology 1019-6439 1791-2423 D.A. Spandidos 10.3892/ijo.2014.2354 ijo-44-06-1831 Articles All trans-retinoic acid (ATRA) induces re-differentiation of early transformed breast epithelial cells ARISIMARIA F.1 STARKERREBECCA A.1 ADDYASANKAR1 HUANGYONG2 FERNANDEZSANDRA V.1 Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107; Section of Gastroenterology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA Correspondence to: Dr Sandra V. Fernandez, Medical Oncology Department, Kimmel Cancer Center, Thomas Jefferson University, 233 South 10th Street, 1002 BLSB, Philadelphia, PA 19107, USA E-mail: sandra.fernandez@jefferson.edu 6 2014 21 03 2014 44 6 1831 1842 23 12 2013 03 02 2014 Copyright © 2014, Spandidos Publications 2014 This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.

Retinoids have been used as potential chemotherapeutic or chemopreventive agents because of their differentiative, anti-proliferative, pro-apoptotic and antioxidant properties. We investigated the effect of all trans-retinoic acid (ATRA) at different stages of the neoplastic transformation using an in vitro model of breast cancer progression. This model was previously developed by treating the MCF-10F human normal breast epithelial cells with high dose of estradiol and consists of four cell lines which show a progressive neoplastic transformation: MCF-10F, normal stage; trMCF, transformed MCF-10F; bsMCF, invasive stage; and caMCF, tumorigenic stage. In 3D cultures, MCF-10F cells form tubules resembling the structures in the normal mammary gland. After treatment with estradiol, these cells formed tubules and spherical masses which are indicative of transformation. Cells that only formed spherical masses in collagen were isolated (trMCF clone 11) and treated with ATRA. After treatment with 10 or 1 μM ATRA, the trMCF clone 11 cells showed tubules in collagen; 10 and 43% of the structures were tubules in cells treated with 10 and 1 μM ATRA, respectively. Gene expression studies showed that 207 genes upregulated in transformed trMCF clone 11 cells were downregulated after 1 μM ATRA treatment to levels comparable to those found in the normal breast epithelial cells MCF-10F. Furthermore, 236 genes that were downregulated in trMCF clone 11 were upregulated after 1 μM ATRA treatment to similar levels shown in normal epithelial cells. These 443 genes defined a signature of the ATRA re-programming effect. Our results showed that 1 μM ATRA was able to re-differentiate transformed cells at early stages of the neoplastic process and antagonistically regulate breast cancer associated genes. The invasive and tumorigenic cells did not show any changes in morphology after ATRA treatment. These results suggest that ATRA could be used as a chemopreventive agent to inhibit the progression of premalignant lesions of the breast.

 breast cancer vitamin A retinoic acid transformation branching Introduction

Vitamin A is obtained through the diet in the form of retinol, retinyl ester or β-carotene (1). Retinoic acid (RA) is one of the principal active metabolites of vitamin A which plays a critical role in cell proliferation, differentiation and apoptosis in normal tissues during embryonic development (2). RA induces differentiation in many cell types and is the most widely used differentiating therapeutic agent (3,4). Retinol has 6 biologically active isoforms that among others includes all-trans (ATRA, tretinoin) and 9-cis RA (alitretinoin); ATRA is the predominant physiological form (5). RA mediates the transcriptional regulation of several genes by binding to the nuclear retinoic acid receptors (RARs), namely RARα, RARβ and RARγ (6,7). Like other nuclear receptors, RARs contain a domain that mediates interaction with ATRA, a zinc finger-containing DNA binding domain that binds to RA response elements (RAREs) in target genes, and a dimerization domain that engages members of the retinoid X receptor (RXR) subfamily in RXR/RAR heterodimers (8). Different isomers activate different receptors and thus lead to different biological effects. RARs can be activated by both all-trans (ATRA) and 9-cis-RA, while RXR are exclusively activated by 9-cis RA; however, due to the conversion of ATRA to 9-cis RA, high concentrations (10−5 M) of ATRA can also activate gene transcription in cells transfected with RXRs (9). It has also been shown that retinoids exert their effects via the nuclear receptor independent pathway (5).

RA and its derivatives are promising anti-neoplastic agents endowed with both therapeutic and chemopreventive potential because they are able to regulate cell growth, differentiation and apoptosis (10,11). It is believed that the anti-neoplastic pathways induced by RA are regulated predominantly by RAR-β, which is known to induce apoptosis; thus it has been suggested that RAR-β plays a critical role in mediating the growth arrest and differentiation in several breast cancer cell types (12–14).

We have developed an in vitro-in vivo model of breast cancer progression by treating the human normal-like breast epithelial cells MCF-10F with a high dose of estradiol (70 nM) (Fig. 1) (15,16). This model consists of four cell lines: i) the spontaneously immortalized cell line MCF-10F, which is considered to be a normal-like breast epithelial cell line; ii) the transformed trMCF cells; iii) the invasive bsMCF cells; and iv) cells isolated from xenografts, caMCFs, which show all characteristics of fully malignant breast cancer cells (Fig. 1). Gene expression studies showed the highest number of deregulated genes in caMCF, being slightly lower in bsMCF, and lowest in trMCF and, this order was consistent with the extent of chromosome aberrations (caMCF>bsMCF>>trMCF) (16). This model of breast cancer progression resembles the different steps of neoplastic transformation of the mammary gland; it is widely held that breast cancer initiates as the premalignant stage of atypical ductal hyperplasia (ADH), progresses into the pre-invasive stage of ductal carcinoma in situ (DCIS), and culminates in the potentially lethal stage of invasive ductal carcinoma (IDC) (17). In collagen, the normal-like MCF-10F cells form tubules resembling the structures observed in the normal mammary gland although after treatment with estradiol, the transformed trMCF cells form tubules and spherical masses, which are indicative of cell transformation (8,19). The spherical masses showed a partial filling of the lumen that would result from decreased central apoptosis, enhanced cellular proliferation or both (18). The filling of the lumen of the tubular structures of the breast is the earliest morphologic alteration and is common in atypical ductal hyperplasia and ductal carcinoma in situ (DCIS) (18). In the presented study, we studied the effect of all trans-RA (ATRA) using this model of breast cancer progression. Our results showed that ATRA was able to re-program early transformed cells to a normal stage.

 Materials and methods Cells and media

The human normal-like breast epithelial cells MCF-10F are estrogen receptor (ER) negative, progesterone receptor (PR) negative and HER2 negative. Cells were cultured in Dulbecco’s modified Eagle’s medium [DMEM/F-12, Gibco, Carlsbad, CA; formula 90–5212 EF: containing DMEM/F12 (1:1) with L-glutamine and phenol red, D-glucose 315 mg/l, sodium pyruvate 55 mg/l] with 5% horse serum, 2.43 g/l sodium bicarbonate, 20 mg/l epidermal growth factor (EGF), 100 mg/l Vibrio cholerae toxin, 10 mg/l insulin, 0.5 mg/l hydrocortisone, 1.05 mM calcium, antibiotics and antimicotic (100 U/ml penicillin, 100 mg/ml streptomycin, 0.25 mg/ml amphotericin). A 10-mM solution of all trans-retinoic acid (ATRA, Cat# R2625, Sigma, St. Louis, MO) was prepared as a stock solution by dissolving ATRA in dimethylsulphoxide (DMSO).

The trMCF clone 11 was isolated by seeding 100–1,000 trMCF cells in a 100-mm cell culture plate and after 1 day in culture, several colonies were isolated by ring cloning. The trMCF clone 11 cells were generated by expanding the cells from one of these colonies; trMCF clone 11 cells only formed spherical masses on collagen. To study the effect of ATRA, trMCF clone 11 cells were treated continuously for 26 days with 10−5 M (10 μM) to 10−8 M (0.01 μM) ATRA (media was replaced daily). As control, the cells were treated with 0.1% DMSO (vehicle). The bsMCF and caMCF cells were treated with 10−5 to 10−8 M ATRA alone or in combination with 2.5 μM 5-aza-dC.

 Collagen assays

The cells were resuspended at a final density of 1.5×104 cells/ml in collagen matrix consisting of 2.68 mg/ml (89.3%) type I collagen (PureCol, Inamed Biomaterials Co., Fremont, CA), 8% 12.5X DMEM-F12 with antibiotics, 0.1 mg/ml insulin, 14 mM NaHCO3 and 0.01 N NaOH. A total of 400 μl (3,000 cells) were plated on the top four 24-well chambers pre-coated with 400 μl of 89.3% collagen mix. Per each treatment, cells were plated in 4 wells and fed daily with the medium described before. The structures in collagen matrix were observed daily under an inverted microscope and at the end of the observation period (8 days), the structures (spherical masses, tubules and intermediate structures) were counted, photographed and fixed in 10% neutral buffered formalin and processed for histological examination. Results were expressed as the total number of structures per well (spherical masses, tubules and intermediate structures) and percentage of the different structures per treatment. The t-test was used to determine if the differences were significant.

 Invasion assays

Cell invasion in real-time were performed using xCELLigence RTCA DP device from Roche Diagnostics (Mannheim, Germany). For this purpose, each well of the upper chamber of the CIM-Plate 16 was covered with Matrigel (BD Biosciences, Franklin Lakes, NJ) basement membrane matrix (1:20 in cell culture media) and 10% fetal bovine serum (chemo-attractant) was added in the lower chamber. A total of 40,000 cells suspended in 100 μl serum free media were seeded per well in CIM-Plates 16 (Roche Diagnostics). Data acquisition and analysis was performed with the RTCA software (version 1.2, Roche Diagnostics). Changes in impedance from cells that invade and migrate to the underside of wells were recorded and monitored for a total of 24 h.

 Gene expression profiling

RNA was isolated from the cells using RiboPure™ kit (Life Technologies, Frederick, MD) and RNA quality was controlled using the Agilent 2100 Bioanalyzer. Gene expression studies were performed using Affymetrix U133 Plus 2.0 (Affymetrix, Santa Clara, CA) human oligonucleotide microarrays containing over 47,000 transcripts and variants, including 38,500 well characterized human genes. After hybridization, the chips were scanned using GeneChip Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Background correction and normalization was done using Iterative Plier 16 with GeneSpring V11.5 software (Agilent, Palo Alto, CA). The criteria for differentially expressed genes was set at ≥2-fold changes (p-value <0.05). The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (Ingenuity Systems, Redwood City, CA) to perform biological network and functional analyses.

 Results Treatment with ATRA induced branching morphogenesis in early transformed breast epithelial cells

MCF-10F cells are normal-like breast epithelial cells that form tubules in collagen matrix (3D culture); when these cells were treated with high dose of estradiol (70 nM), the cells (trMCF) formed tubules and spherical masses. To isolate transformed cells that only form spherical masses, trMCF cells were seeded at low density in cell culture dishes and several clones were isolated by ring cloning. One of these clones, trMCF clone 11, did not form tubules in collagen; instead these cells formed spherical masses and intermediate structures (Fig. 2A and B). The trMCF clone 11 cells were treated continuously for 26 days with 10−5 to 10−8 M all trans-retinoic acid (ATRA) and, we found that cells treated with 10−5 and 10−6 M ATRA were able to form tubules in collagen (Fig. 2C and D). Furthermore, the spherical masses formed by trMCF clone 11 treated with 10−5 and 10−6 M ATRA (Fig. 2C and D) were smaller compared to the ones formed by the controls (Fig. 2A and B) or cells treated with 10−7 and 10−8 M ATRA (Fig. 2E and F). The trMCF clone 11 cells treated with 10−7 and 10−8 M ATRA (Fig. 2E and F) did not show any difference in morphology when compared to the controls (Fig. 2A and B). The number of spherical masses, intermediate structures and tubules for trMCF clone 11 cells treated with different concentrations of ATRA was counted (Fig. 3). The total number of structures in collagen was significantly lower in cells treated with ATRA compared with the controls suggesting that ATRA treatment decrease the proliferation rate of the cells (p<0.01) (Fig. 3A). The control trMCF clone 11 showed spherical masses and intermediate structures but no tubules in collagen while cells treated with 10−6 and 10−5 M ATRA formed tubules and less spherical masses (Fig. 3A). The cells treated with 10−5 or 10−6 M ATRA formed significantly less spherical masses than the cells treated with 10−7 or 10−8 M ATRA (p<0.01) (Fig. 3A). A total of 43% of the structures were tubules in the wells containing cells treated with 10−6 M ATRA and 10% tubules in wells with 10−5 M ATRA-treated cells (Fig. 3B).

The invasion capacity of trMCF clone 11 was studied before and after ATRA treatment but, no differences were observed (Fig. 4). The bsMCF and caMCF cells did not show any changes in their morphology or invasion capacity after treatment with ATRA alone or in combination with the demethylating agent 5-aza-cytidine (data not shown).

 Treatment with ATRA re-programmed gene expression of early transformed cells

As trMCF clone 11 cells that only formed spherical masses on collagen were able to form tubules after treatment with 10−5 or 10−6 M ATRA, gene expression studies were performed on these cells. The microarray data have been deposited into the NCBI gene expression omnibus (GEO) datasets (GSE51549). The unsupervised sample classification by PCoA (principle coordinate analysis) revealed that trMCF clone 11 cells treated with 10−5 or 10−6 M ATRA demonstrated a major difference with trMCF clone 11 cells, and a minor difference with MCF-10F; also sample differences between 10−5 M ATRA and 10−6 M ATRA were weak (Fig. 5). Although, trMCF clone 11 cells treated with 10−5 M ATRA and 10−6 M ATRA showed minor differences at the expression level, we considered trMCF clone 11 treated with 10−6 M ATRA for the expression analysis since the number of tubules in collagen matrix was higher for this concentration (43% tubules with 10−6 M ATRA vs. 10% tubules with 10−5 M ATRA). For gene expression studies, three experimental groups were compared using empirical Bayesian-moderated t-test implemented in R package ‘limma’: the normal breast epithelial cells MCF-10F, the cells transformed by treatment with estradiol trMCF clone 11 (that only formed spherical masses on collagen) and the trMCF clone 11 after treatment with 10−6 M ATRA. We generated three gene lists at criteria of fold change ≥2 and p≤0.05: gene list-1 (trMCF clone11 vs. MCF-10F) with 1,409 probes (613 probes upregulated; 796 probes downregulated), gene list-2 (ATRA trMCF clone 11 vs. trMCF clone 11) with 1,859 probe sets (1,053 probes upregulated; 806 probes downregulated) and gene list-3 (ATRA trMCF clone 11 vs. MCF-10F) with 870 probe sets (308 probes upregulated; 562 probes downregulated) (Fig. 6). Most importantly, 207 genes (271 probes) upregulated in the transformed trMCF clone 11 (compared to the normal MCF-10F) were downregulated after treatment with 10−6 M ATRA (Fig. 6 and Table IA) and 236 genes (316 probes) that were downregulated in trMCF clone 11 (compared to MCF-10F) were upregulated by 10−6 M ATRA treatment (Fig. 6 and Table IB). These 443 genes defined a gene signature programming the reverse-transformation effect by ATRA (Table I). The relatively smaller number of significant probe sets in gene list-3 compared with other gene lists (Fig. 6) further supported the findings that ATRA-treatment reprograms the gene expression status of trMCF clone 11 cells to MCF-10F.

Ingenuity pathway analysis (IPA) revealed 4 canonical pathways significantly dysregulated in the transformed cells trMCF clone 11: aryl hydrocarbon receptor signaling, retinoic acid activation, xenobiotic metabolism signaling and molecular mechanism of cancer (Table II). Several genes of these pathways that were up- or downregulated in trMCF clone 11 show similar levels of expression to MCF-10F after trMCF clone 11 was treated with 10−6 M ATRA (Table II and Fig. 7). Genes from the aryl hydrocarbon receptor signaling ALDH1A3, CCND1, TGFBR2, TGM2 and TFDP1 were downregulated in the transformed cells trMCF clone 11 when compared to their expression in the normal breast epithelial cells MCF-10F and, the expression of these genes was upregulated after these cells were treated with 10−6 M ATRA reaching similar levels to the expression in MCF-10F (Table II and Fig. 7). One of the functions that show enrichment of dysregulated genes in the transformed trMCF clone 11 cells is cell morphology and the expression of most of these genes reached similar levels to MCF-10F after trMCF cells were treated with 10−6 M ATRA. The expression of some genes related to cell morphology such as PLD1, CD44, STX6, STMN3, ATF2, ETS2, NEK2, HAS3, MGP, GNA13 were upregulated in the transformed trMCF clone 11 and their expression reached normal levels after 10−6 M ATRA treatment (Fig. 7); other genes related to cell morphology such as PHLDA1, GBP1, HS6ST2 and TLR3 were downregulated in trMCF clone 11 and their expressions increased after 10−6 M ATRA treatment reaching similar levels to those found in the normal MCF-10F breast epithelial cells (Fig. 7). Also, the expression of several genes that encode enzymes involved in chromatin modifications such as MGEA5, ATF-2, KDM5B, PRMT2 (PRM2), PHF21A and NSD1, were dysregulated in trMCF clone 11, reaching normal levels after 10−6 M ATRA treatment (Fig. 7).

 Discussion

In this study we showed that all trans-retinoic acid (ATRA) induced branching of early transformed human breast epithelial cells. The transformed trMCF clone 11 cells form spherical masses in collagen (3D culture) and treatment with 10−6 M ATRA produced a significant decrease in spherical masses and an increased number of tubules. Cells at an advanced stage of transformation (bsMCF and caMCF) did not show any change in morphology after being treated with ATRA. Our previous results showed that RARβ (retinoic acid receptor β) was unmethylated in MCF-10F and trMCF cells and became hypermethylated at the invasive (bsMCF) and tumorigenic (caMCF) stages (19); although bsMCF and caMCF were treated with 5-aza-dC to reactivate the expression of RARβ in combination with ATRA, no changes in the phenotype of these cells in collagen were observed. Our results indicate that ATRA is able to re-differentiate early transformed cells to a normal stage but, not tumor cells at later stages of the neoplastic process. We previously showed that bsMCF and caMCF had important chromosomal gains and losses and the earlier transformed cells trMCF showed small genomic changes (16); this could explain why ATRA was only effective as a re-differentiation agent in the early transformed breast epithelial cells. Different studies indicate that epigenetic modifications play important roles in RA transcriptional regulation (20–24). Histones have a long N-terminal tail extending outside the nucleosome that is subject to acetylation, phosphorylation, and methylation (25). In the absence of RA, co-repressive elements (SMRT, NCoR and SIN3A) inhibit transcription; the presence of RA releases co-repressors and histone deacetylases allowing chromatin remodeling and access to specific RAREs (20,24). RA treatment leads to acetylation of histones H3 and H4 that lead to a more open stage of the chromatin allowing the transcription of ATRA regulated genes. However, only a limited number of information is currently available on the epigenetic dynamics of RA response.

Recently, analysis of gene expression array datasets of different FDA approved drugs revealed that ATRA (tretinoin) is a drug that is negatively associated with cancer stem cell (CSC) enriched gene expression signature (26). We found that ATRA treatment reduced the expression of the stem cell marker CD44 in early transformed cells. ATRA exerts effects on stem cell differentiation in part via the modulation of the epigenome. Numerous enzymes that alter the modifications on histones are involved in transcriptional activation of specific genes in stem cells, and many of these enzymes are modulated by RA treatment of stem cells (27). The expression of several genes encoding enzymes involved in chromatin modifications such as MGEA5, ATF-2, KDM5B, PRMT2, PHF21A and NSD1 were dysregulated in trMCF clone 11, reaching normal levels after ATRA treatment. Others have shown that in breast cancer, retinoids are effective inhibitors of breast cancer cells at early stages of tumor progression, but their effectiveness diminishes as the tumors become more aggressive (28). Our results support these findings.

Our results show that the RA concentration is important to induced re-differentiation of early transformed breast epithelial cells. The treatment of transformed cells with either 10−7 or 10−8 M ATRA did not induced any change in morphology although, cells were able to form tubules after treatment with 10−5 and 10−6 M ATRA, more tubules being developed after treatment with 10−6 M (1 μM) ATRA.

Little is known about the genomic targets and effects of the different isoforms of the RARs and mechanism or extent of crosstalk between RA signaling and other signaling pathways. It has been recently shown that RAR binding through the genome is highly coincident with estrogen receptor α binding, resulting in widespread crosstalk of RA and estrogen signaling to antagonistically regulate breast-cancer associated genes (29). Our gene expression studies determined 443 genes which defined a signature of ATRA re-programming effect in early transformed breast epithelial cells; these genes were dysregulated in the early transformed cells and they reached normal levels after the cells were treated with 10−6 M ATRA. Genes from the aryl hydrocarbon receptor (AhR), retinoic acid receptor (RAR) and the xenobiotic pathways were dysregulated in the early transformed breast epithelial cells and their expression reached normal levels after ATRA treatment. It has been shown that there is an interaction between AhR and RAR activation and that AhR not only binds to polycyclic aromatic hydrocarbon family of environmental contaminants but also to some synthetic retinoids (30,31).

N-(4-hydoxyphenyl) retinamide (fenretinide or 4HPR) is a synthetic retinoid that is currently one of the most promising clinically tested retinoids. The modification of the carboxyl end of all-trans RA with N-4-hydroxyphenyl group resulted in increased efficacy as a chemoprevention agent as well as reduced toxicity when compared with other retinoids (32). Animal models have demonstrated that treatment with fenretinide prevents chemically induced cancers of the breast, prostate, bladder and skin (33–36).

In conclusion, our results showed that 1 μM ATRA was able to re-differentiate transformed cells at early stages of the neoplastic process and antagonistically regulated breast cancer associated genes. Our results support previous findings that 1 μM ATRA could be used as a chemo-preventive agent to inhibit the progression of premalignant lesions of the breast.

We thank Karen Trush for helping in the preparation of the final figures. This study was supported by The Pennsylvania Breast Cancer Coalition and Friends for an Earlier Breast Cancer Test.

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In vitro-in vivo model of cell transformation. The human normal-like MCF-10F cells were treated with high dose of estradiol and named early transformed breast epithelial cells (trMCF). The trMCF cells were seeded on a Boyden chamber and the cells that invaded, bsMCF, were selected and expanded. The bsMCF cells were injected in the fat mammary pad of SCID mice producing breast tumor xenografts. These xenografts were surgically removed and tumor cells were expanded giving origin to caMCF. The trMCF cells did not produced tumors when injected in SCID mice.

All-trans retinoic acid (ATRA) induces morphological changes in transformed cells trMCF clone 11. The trMCF clone 11 cells were plated in collagen matrix (3-D cultures) after being treated continuously for 26 days with different concentrations of ATRA. The cells were photograph after 8 days in collagen. (A) trMCF clone 11 cells (control); (B) trMCF clone 11 cells treated with 0.1% DMSO (vehicle, control); (C) trMCF clone 11 after being treated with 10−5 M (10 μM) ATRA; (D) trMCF clone 11 cells after being treated with 10−6 M (1 μM) ATRA; (E) trMCF clone 11 cells after being treated with 10−7 M ATRA; (F) trMCF clone 11 cells after being treated with 10−8 M ATRA.

Spherical masses, tubules and intermediate structures formed in collagen by trMCF clone 11 before and after ATRA treatments. The trMCF clone 11 cells form spherical masses in collagen and some intermediate structures. The trMCF clone 11 cells were treated with different concentrations of all-trans retinoic acid (ATRA) for 26 days; after ATRA treatments, the cells were plated in collagen. (A) Total number of different structures in collagen of trMCF clone 11 cells before and after ATRA treatment. Total number of spherical masses (SM), tubules and intermediate structures (spherical masses with prolongations) per well are shown. (B) Different structures on collagen matrix of trMCF clone 11 cells after treatment with different concetrations of ATRA. Percentage of different structures in collagen.

Invasion assay of trMCF clone 11 before and after ATRA treatments. The cell index of Matrigel-coated wells (invasion) at different time points are shown. The invasion capacity of the trMCF clone 11 did not show significant differences after 10−5 M ATRA (▲) or 10−6 M ATRA (■) compared with control after 16 h.

Unsupervised sample classification by principle coordinate analysis (PCoA). Two arrays were performed for each cell line and treatment: MCF-10F (MCF_CTR1 and MCF_CTR2), trMCF clone 11 (E2_CTR1 and E2_CTR2), 10−5 M ATRA trMCF clone 11 (E2_Hi1 and E2_Hi2) and 10−6 M ATRA trMCF clone 11 (E2_Lo1 and E2_Lo2). The trMCF clone 11 cells treated with 10−5 M ATRA (E2_Hi) or 10−6 M ATRA (E2_Lo) shown a major difference with trMCF clone 11 cells (E2_CTR) and minor differences with MCF-10F cells (MCF_CTR).

Representation of the gene expression studies showing number of dysregulated genes. Expression studies were performed in the early transformed trMCF clone 11 cells before and after treatment with 10−6 M ATRA (ATRA trMCF clone 11) and normal human breast epithelial MCF-10F cells. A total of 207 genes upregulated in the transformed trMCF clone 11 (compared to the normal MCF-10F) were downregulated after treatment with 10−6 M ATRA and, 236 genes that were downregulated in trMCF clone 11 (compared to MCF-10F) were upregulated by 10−6 M ATRA treatment. These 443 genes defined a gene signature programming the reverse-transformation effect by ATRA.

Heat map of selected genes in normal breast epithelial cells and early transformed cells before and after 10−6 M ATRA treatment. The expressions of genes involved in cell morphology are shown; also some genes from the aryl hydrocarbon and RAR pathways and genes involved in chromatin modification are shown. The genes that were dysregulated in the early transformed breast epithelial cells (trMCF clone 11) reached normal levels, similar to the normal breast epithelial cells MCF-10F, after treatment with 10−6 M ATRA. Red, yellow or blue colors represent expression levels above, at or below the mean level across the samples.

Gene signature programming.

A, ATRA-downregulated genes (207 genes).

ACSS3 DNAJB9 KLF11 PL-5283/SLC13A4 TIMP3a
ALDH3A2 DSC3 KLHDC8B PLAG1 TMEM167B
ALDOC DUSP5P LCA5 PLD1 TMEM27
ALPK1 EFHC1 LOC100288092 PLD6 TMEM40
ANKRD37 EFNB3 LOC100289187 PLK1S1 TMEM59
AQPEP EPB41L4B LOC100505894 POFUT2 TNFRSF25
ARG2 ERCC1a LOC100506057/STK32C POLR1D TNFSF11
ARHGAP19 ETS2a LOC100507303 PPIL6 TNKS
ARHGEF10 FABP6 LOC100507547 PPOX TP63
ATF2 FAM117A LOC100507644 PPP1R13L TPD52L1a
ATG14 FAM168A LOC439938 PPP1R3C TPRG1
ATP2C2 FAM46C LOC642587 PRKAB2 TRAF3IP2
ATP5C1 FAT2 LOX PRMT2 TRAPPC6A
BCAS4 FBXO2 LRIG1 PROCR TSC22D3
BFSP1 FEM1B LYST PTEN TTBK2
BLNK FLCN MAP2K5 PTEN/PTENP1 TTC39B
BTBD3 FLJ37644 MAPT PTPN14 TXNIP
C11orf80 FLJ45244 MGEA5 RAB11FIP4 UFM1
C16orf46 FNBP1L MGPa RAB38 UGT1A1/1A4/1A6/1A8/1A9/1A10
C17orf39 FNTA MLF1 RAB40C USP3
C17orf48 FNTB MRAP2 RAB4A USP32
C1orf133 FSIP1 MXD1 RAB7L1 VPS8
C1orf161 FXYD2 MYLIP RASSF6 WAC
C20orf111 GBAS N4BP2L1 RMND1 WDR59
C21orf7 GGNBP2 NDE1 RNF169 WDR91
C5orf41 GGTA1 NDUFB4 SCARA3 WWOXa
C7orf68 GIT2 NEK2 SCRG1 YOD1
C9orf9 GJA3 NEURL1B SEMA6A ZBTB34
CCDC28A GKAP1 NFKBIL1 SFT2D1 ZFAND5
CD44a GNA13 NGLY1 SHOX2 ZNF836
CELSR2 GNAI1 NMNAT3 SLC25A37 ZNRF1
CLCA2 GOSR2 NPL SLC2A12
CMBL GPM6A OGFRL1 SLC2A9
COBL GPNMB PALMD SLC5A3
CRIP2 H19 PDCD4a SOCS3
CSNK2A2 HAS3 PDCD5 SORL1
CYP1B1 HBP1 PDE7A SPATA17
CYP39A1 HERPUD1 PDZD2 STAU2
DBP HMGCL PER1 STMN3
DCD IFNAR1 PER3 STX6
DDAH2 IRF6 PHF21A SUSD4
DDCa IRX2 PHLDB3 TESK2
DDIT3 KCMF1 PHTF2 THBS2
DHX40 KDM5B PIK3CD THSD1///THSD1P1

Genes upregulated in trMCF clone 11 that were downregulated after 10−6 M ATRA-treatment to similar levels found in MCF-10F are indicated.

Genes with binding sites for RARα or RARβ described by Hua et al (29).

B, ATRA-upregulated genes (236 genes).

ABHD13 COX7B HIATL1 OSTM1 SLC43A3 TSPAN2
ACP2 CRELD2 HIGD1A P2RY2 SMPDL3A UBE2Na
ADAM12 CST6a HOXA11 PAPPA SNRNP25 UBE2Q1
ALDH1A3 CSTF2 HPGD PARVA SNX19 UBP1
ANO1 CYB561D2 HS3ST1 PCSK5 SOAT1 UNK
AOX1 DCBLD2 HS6ST2 PDE12 SPAG1 VARS2
APOL6 DHRS9 IFI44 PHACTR3 SPATA13 VGLL3
ARGLU1 DHX9 IFIT3 PHLDA1 SRPX2 VSIG10
ARHGAP26 DNAJA1 IFIT5 PHLDA2 SRSF10 ZADH2
ARHGAP42 DOLK IFNAR1 PITPNC1 SRSF2IP ZBED4
ARHGDIB DPH3 KHNYN PKIB SSPN ZDHHC2
ARIH2 EFCAB2 KLHL18 PLCXD2 STK39 ZMPSTE24
ASPHD2 EFNB2 KLHL23 PLGLA/PLGLB1/PLGLB2 STS ZNF252
ATP6V0A2 EHD4 KRT80 PNO1 STYK1 ZNF271
B3GALNT1 EIF2AK1 LOC100131993 PNPLA3 SUPT7L ZNF326
BRI3BP EIF5B LOC100505759 PODXL SUSD5 ZNF35
BTG1 ELOVL6 LOC100507192 POLR3K SYNCRIP
C12orf26 ENC1a LOC283278 PPP2R1B SYNJ2BP
C12orf5 ENY2 LOC728903 PRPS1 SYTL2
C1GALT1C1 ERLIN2 MACC1 PRR15 SYTL5
C1orf116 EXOG MARCKS PSCA TBC1D30
C1orf135 FADS1a MAT2A PSME3 TFDP1
C1orf212 FAIM MCFD2 PTGR1 TFRC
C1orf226 FAM118B MEIS3P1 PTP4A2 TGFB2
C6orf223 FAM119A MFAP3L PTPRB TGFBR2a
CALM1a FAM83A MFI2 PTPRJ TGM2
CCDC68 FBXW2 MFSD1 RABIF THSD4
CCDC88A FDX1 MICALL1 RBM25 TIMM23
CCND1a FN1a MMACHC RBM45 TIMM8A
CDA FNIP2 MRPL35 RGS17 TIMM8B
CDC42EP2 FRMD3 MST1R RHOBTB1 TLCD1
CDH2 FUCA1 MTERFD3 RHOF TLR3
CEP78 FXN MYEOV RPL27A TLR4
CFH/CFHR1 FZD8 MYO5C RPS6KA2 TMC5
CFI GALNT7 NAA40 S1PR3 TMEM133
CHAC2 GATAD2A NAV3 SAMHD1 TMEM177
CHML GBP1 NECAP1 SCEL TMEM9B
CHRNA5 GDA NIPAL1 SGK223 TP53I3
CLDN23 GGCX NMI SH3TC2 TPCN2
CMAH GPATCH2 NRP2 SLC16A5 TRAK2
CNPY2 GPX8 NSD1 SLC1A1 TRIM45
COL4A3 GXYLT1 OLAH SLC35B4 TRIOBP
COL4A4 HAS2 OR7E14P SLC35C1 TRNT1
COX7A1 HERC6 OR7E47P SLC37A1 TSPAN12

Genes downregulated in trMCF clone 11 that were upregulated after 10−6 M ATRA-treatment to similar levels found in the normal breast epithelial cells MCF-10F.

Genes with binding sites for RARα or RARβ described by Hua et al (29).

Canonical pathways enriched with differentially expressed genes.

trMCF clone 11 vs. MCF-10F ATRA trMCF clone 11 vs. trMCF clone 11
Aryl hydrocarbon receptor signaling ALDH1A3↓, CCND1↓, TGFBR2↓, TGM2 ↓, TFDP1↓, ALDH3A2↑, CYP1B1↑ ALDH1A3↑, CCND1↑, TGFB2↑, TGM2↑,TFDP1↑, ALDH3A2↓, CYP1B1↓
Other genes: CDKN1A↓, JUN↓ ALDH7A1↑, CSNK2A1↑, TGFB1↑, MAPK1↑, NFE2L2↑ Other genes: CCNE1↑, CCNE2↑, CDK6↑,DHFR↑, IL1B↑, IL6↑, NR2F1↑, NRIP1↑, POLA1↑ ALDH3B2↓, ARNT↓, NCOA3↓, HSPB2↓, ALDH6A1↓
RAR activation ALDH1A3↓, DHRS9↓, NSD1↓, TGFB2↓, CSNK2A2↑, PIK3CD↑, PRMT2↑, PTEN↑ ALDH1A3↑, DHRS9↑, NSD1↑, TGFB2↑, CSNK2A2↓, PIK3CD↓, PRMT2↓, PTEN↓
Other genes: JUN↓, NR2F2↓, RBP1↓, CSNK2A1↑, CSNK2A2↑, MAPK1↑, MAPK14↑, TGFB1↑, GNAS↑ Other genes: GTF2H2↑, IGFBP3↑, MAP2K1↑, MAPK13↑, NR2F1↑, NRIP1↑, RKAR2B↑, DH10↑, CITED2↓, PNRC1↓, PRKAR1A↓, SMARCD2↓
Xenobiotic metabolism signaling ALDH1A3↓, HS3ST1↓, HS6ST2↓, PPP2R1B↓, ALDH3A2↑, CYP1B1↑, MAP2K5↑, PIK3CD↑, UGT1A1 (and others UGT)↑ ALDH1A3↑, HS3ST1↑, HS6ST2↑, PPP2R1B↑, ALDH3A2↓, CYP1B1↓, MAP2K5↓, PIK3CD↓, UGT1A1 (and others UGT)↓
Other genes: CHST15↓, ALDH7A1↑, CAMK1D↑, HDAC4↑, MAPK1↑, MAPK14↑, MGMT↑, UGT8↑, NFE2L2↑ Other genes: ILIB↑, IL6↑, NRIP1↑, MAP2K1↑, MAPK13↑, ALDH3B2↓, ARNT↓, CAMK2D↓, CITED2↓, MAP3K8↓, PPP2R3A↓, ALDH6A1↓, MAP3K2↓
Molecular mechanisms of cancer TGFB2↓, TGFBR2↓, CCND1↓, FZD8↓, PLCB4↓, RABIF↓, RHOF↓, GNA13↑, GNAI1↑, CD44↑ TGFB2↑, TGFBR2↑, CCND1↑, FZD8↑, PLCB4↑, RABIF↑, RHOF↑, GNA13↓, GNAI1↓, CD44↓
Other genes: CDKN1A↓, CTNNB1↓, FYN↓, IRS1↓, JUN↓, SMAD4↓, TCF4↓, XIAP↓, PIK3CD↑, TCF3↑, TGFB1↑, GNAL↑, MAPK1↑, MAPK14↑ Other genes: APC↑, CCNE1↑, CCNE2↑, CDC25A↑, CDK6↑, CYCS↑, E2F2↑, MAP2K1↑, MAPK13↑, PRKAR2B↑, RAPGEF3↑, RBL1↑, TFDP1↑, ARHGEF10↓, FOXO1↓, HHAT↓, IRS1↓, NF1↓, PAK3↓, PIK3CD↓, PRKAR1A↓, RALGDS↓, RHOV↓

Genes downregulated (↓) or upregulated (↑) are shown. ATRA trMCF clone 11 refers to trMCF clone 11 treated with 10−6 M ATRA.