Basal-like Cell Lines Research Articles

Linc00152 promotes tumorigenesis by regulating DNMTs in triple-negative breast cancer

Long noncoding RNA (lncRNA) is a significant factor that regulates various aspects of genome activity, including tumor development and progression. Linc00152, a member of lncRNA, is unregulated in various types of cancer. However, its role in breast cancer, especially in triple-negative breast cancer (TNBC), is unclear. In this study, we found that linc00152 was highly expressed in all basal-like cell lines and in the majority of TNBC tissues. Linc00152 suppression by shRNA significantly inhibited invasion and colony growth. Such suppression also triggered apoptosis in vitro and inhibited tumor growth in vivo. We also revealed that linc00152 partially enhanced breast cancer tumorigenesis by inactivation of the BRCA1/PTEN through DNA methyltransferases. This study provides new insight regarding linc00152 as a promising biomarker and therapeutic target for human TNBC treatment.

The IL-17B-IL-17 receptor B pathway promotes resistance to paclitaxel in breast tumors through activation of the ERK1/2 pathway.

Interleukin 17B (IL-17B) is a pro-inflammatory cytokine that belongs to the IL-17 cytokines family and binds to IL-17 receptor B (IL-17RB). Here we found that high expression of IL-17B and IL-17RB is associated with poor prognosis in patients with breast cancer and that IL-17B expression upregulation is specifically associated with poorer survival in patients with basal-like breast cancer. We thus focused on IL-17B role in breast cancer by using luminal and triple negative (TN)/basal-like tumor cell lines. We found that IL-17B induces resistance to conventional chemotherapeutic agents. In vivo, IL-17B induced resistance to paclitaxel and treatment with an anti-IL-17RB neutralizing antibody completely restored breast tumor chemosensitivity, leading to tumor shrinkage. We next focused on the signaling pathways activated in human breast cancer cell lines upon incubation with IL-17B. We observed that IL-17B induces ERK1/2 pathway activation, leading to upregulation of anti-apoptotic proteins of the BCL-2 family. IL-17B-induced chemoresistance was completely abolished by incubation with PD98059, an inhibitor of the MAPK/ERK pathway, indicating that the ERK pathway plays a crucial role. Altogether our results emphasize the role of the IL-17B/IL-17RB signaling pathway in breast tumors and identify IL-17B and its receptor as attractive therapeutic targets for potentiating breast cancer chemotherapy.

Inhibition of basal-like breast cancer growth by FTY720 in combination with epidermal growth factor receptor kinase blockade

BackgroundNew molecular targets are needed for women with triple-negative breast cancer (TNBC). This pre-clinical study investigated the combination of the EGFR inhibitor gefitinib with the sphingosine kinase (SphK) inhibitor FTY720 (Fingolimod), aiming to block tumorigenic signaling downstream of IGFBP-3, which is abundantly expressed in basal-like TNBC.MethodsIn studies of breast cancer cell growth in culture, proliferation was monitored by IncuCyte live-cell imaging, and protein abundance was determined by western blotting. In vivo studies of mammary tumor growth used two models: orthotopic xenograft tumors derived from three basal-like TNBC cell lines, grown in immune-deficient mice, and syngeneic murine 4T1 tumors grown in immune-competent mice. Protein abundance in tumor tissue was assessed by immunohistochemistry.ResultsQuantitated by live-cell imaging, the inhibitor combination showed synergistic cytostatic activity in basal-like cell lines across several TNBC molecular subtypes, the synergy being decreased by IGFBP-3 downregulation. Suppression of the tumorigenic mediator CD44 by gefitinib was potentiated by FTY720, consistent with CD44 involvement in the targeted pathway. In MDA-MB-468 and HCC1806 orthotopic TNBC xenograft tumors in nude mice, the drug combination inhibited tumor growth and prolonged mouse survival, although this effect was not significant for the gefitinib-resistant cell line HCC70. Combination treatment of murine 4T1 TNBC tumors in syngeneic BALB/c mice was more effective in immune-competent than immune-deficient (nude) mice, and a relative loss of tumor CD3 (T-cell) immunoreactivity caused by FTY720 treatment alone was alleviated by the drug combination, suggesting that, even at an FTY720 dose causing relative lymphopenia, the combination is still effective in an immune-competent setting. Immunohistochemistry of xenograft tumors showed significant enhancement of caspase-3 cleavage and suppression of Ki67 and phospho-EGFR by the drug combination, but SphK1 downregulation occurred only in MDA-MB-468 tumors, so is unlikely to be integral to treatment efficacy.ConclusionsOur data indicate that targeting IGFBP-3-dependent signaling pathways through gefitinib-FTY720 co-therapy may be effective in many basal-like breast cancers, and suggest tissue IGFBP-3 and CD44 measurement as potential biomarkers of treatment efficacy.

Impact of inducible nitric oxide synthase (iNOS) expression on triple negative breast cancer outcome and activation of EGFR and ERK signaling pathways.

Inflammation is implicated in triple negative breast cancer (TNBC) progression. TNBC carries a worse prognosis than other breast cancer subtypes, and with the clinical and molecular heterogeneity of TNBC, there is a lack of effective therapeutic targets available. Identification of molecular targets for TNBC subtypes is crucial towards personalized patient stratification. Inducible nitric oxide synthase (iNOS) has been shown to induce p53 mutation accumulation, basal-like gene signature enrichment and transactivation of the epidermal growth factor receptor (EGFR) via s-nitrosylation. Herein we report that iNOS is associated with disease recurrence, distant metastasis and decreased breast cancer specific survival in 209 cases of TNBC. Employing TNBC cell lines representing normal basal breast, and basal-like 1 and basal-like 2 tumors, we demonstrate that nitric oxide (NO) induces EGFR-dependent ERK phosphorylation in basal-like TNBC cell lines. Moreover NO mediated cell migration and cell invasion was found to be dependent on EGFR and ERK activation particularly in basal-like 2 TBNC cells. This occurred in conjunction with NF-κB activation and increased secretion of pro-inflammatory cytokines IL-8, IL-1β and TNF-α. This provides substantial evidence for EGFR as a therapeutic target to be taken into consideration in the treatment of a specific subset of basal-like TNBC overexpressing iNOS.

Abstract 3064: Retinoic acid: An effective therapy for basal-like breast cancer

Abstract We have identified a novel strategy to identify breast cancer patients who will benefit from an existing anti-cancer agent, retinoic acid (RA). While RA has not yet achieved success in the treatment of breast cancers, we hypothesized that it can be an effective therapy for a subset of triple-negative breast cancer (TNBC) patients. TNBC is among the most aggressive breast cancers, and lacks targeted therapies. TNBCs can be further subtyped into basal-like and claudin-low, which differ in gene expression and drug sensitivities. Understanding the molecular basis of these subtypes will lead to the development of more effective treatment options for TNBC. To test this hypothesis, we performed tumor growth assays on TNBC cell lines and patient-derived xenografts (PDXs). We found that RA treatment decreased the tumor growth of four basal-like TNBC cell lines (MDA-MB-468, HCC70, SUM149, HCC1937). In contrast, RA increased the tumor growth of two claudin-low TNBC cell lines (MDA-MB-231, MDA-MB-436). Gene expression and methylation analysis of these affected cell lines revealed subtype-specific expression of RA-inducible genes due to silencing by DNA methylation, e.g. of the RA-inducible tumor-suppressor gene RARRES1. RARRES1 is silenced by methylation in claudin-low cell lines, but is hypomethylated and expressed in basal-like cells. Use of the subtype-specific expression and methylation profiles allowed us to accurately predict the response of 4 PDXs to RA treatment. Continued classification of TNBCs into these two subtypes will enable clinical use of RA, in part due to the subtype-specific hypomethylation of RA-inducible tumor suppressor genes including RARRES1. We have identified additional subtype-specific biomarkers which can predict the response of patient tumors to RA treatment, thus identifying a novel targeted therapy strategy for TNBCs. Citation Format: Krysta Mila Coyle, Cheryl A. Dean, Dejan Vidovic, Ian C. Weaver, Carman A. Giacomantonio, Paola Marcato. Retinoic acid: An effective therapy for basal-like breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3064. doi:10.1158/1538-7445.AM2017-3064

Abstract 1747: A microenvironment gene signature predicts poor outcome in patients with luminal breast cancers subjected to local-regional treatment

Abstract Gene expression studies, mainly addressed at the tumor cell compartment of breast cancers (BC) contributed to unravel the molecular heterogeneity providing clinicians with new and reliable tools for therapeutic planning. Despite many investigations have focused on genetic abnormalities initiating and driving tumorigenesis, there is now evidence that the cancer cell behavior depends not only on intrinsic features, but also on the interactions with the microenvironment. However, notwithstanding the interest in investigating tumor-stroma cross-talks, the clinical relevance of subtype-specific molecular imprint of such interactions is largely unexplored. As such, we attempted to clinically and biologically validate the subtype-specific gene signatures derived from an in vitro model recapitulating the interaction between BCs and activated stromal cells. Gene expression signatures derived from luminal (T47D, MCF7, ZR75.1), HER2+ (SkBr3+, BT474, MDA-MB-361) and basal-like (MDA-MD-468, MDA-MB-231, BT20) cell lines treated by conditioned media from normal or cancer-associated fibroblasts (CAFs) showed common- and subtype-specific pathways according to GSEA. In fact, interferon, IL-6, IL-12 and IL-23 signaling, Toll Like Receptor pathway, pathways related to inflammation and metabolism of carbohydrates were positively enriched in HER2+ and luminal subtypes. Complement cascade and Tumor Necrosis Factor pathways were positively enriched in basal and luminal tumors; no common pathway was observed in HER2+ and basal subtypes. The association between microenvironment signatures specific for luminal, HER2+ and basal BC cell lines and disease-free survival was evaluated in silico on published gene expression profiles (GEPs) from 2048 patients homogeneously treated. BCs were classified as microenvironment-positive (µENV+ve, with GEP suggesting stroma activation), or negative (µENV-ve) by correlating tumor’s GEP with the respective subtype-specific signature. Patients with luminal µENV+ve tumors had 2.5-fold higher risk of developing distant metastases (HR=2.546; 95% Confidence Interval, Cl: 1.751-3.701, P=9.84E-07), while µENV status did not affect or was only suggestive of metastases in women with HER2-enriched (HR=1.541; 95% Cl: 0.788-3.012, P=0.206) or basal tumors (HR=1.894; 95% Cl: 0.938-3.824; P=0.0747), respectively. In luminal tumors, the µENV status maintained its prognostic role (HR=2.098; CI: 1.214-3.624; P=0.00791) in multivariable analysis including size, age and genomic grade index. Validity of our in vitro model was also supported by biological endpoints such as proliferation (MTT-assay) and migration/invasion (Transwell-assay). In vitro-derived gene signatures trace a subtype-specific interaction with CAFs and add independent information to classical prognostic variables in women with luminal “microenvironment sensitive” tumors. Citation Format: Maria Grazia Daidone, Giuseppe Merlino, Patrizia Miodini, Maurizio Callari, Vera Cappelletti. A microenvironment gene signature predicts poor outcome in patients with luminal breast cancers subjected to local-regional treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1747. doi:10.1158/1538-7445.AM2017-1747

Patterns of cell cycle checkpoint deregulation associated with intrinsic molecular subtypes of human breast cancer cells

Genomic instability is a hallmark of breast cancer, contributes to tumor heterogeneity, and influences chemotherapy resistance. Although Gap 2 and mitotic checkpoints are thought to prevent genomic instability, the role of these checkpoints in breast cancer is poorly understood. Here, we assess the Gap 2 and mitotic checkpoint functions of 24 breast cancer and immortalized mammary epithelial cell lines representing four of the six intrinsic molecular subtypes of breast cancer. We found that patterns of cell cycle checkpoint deregulation were associated with the intrinsic molecular subtype of breast cancer cell lines. Specifically, the luminal B and basal-like cell lines harbored two molecularly distinct Gap 2/mitosis checkpoint defects (impairment of the decatenation Gap 2 checkpoint and the spindle assembly checkpoint, respectively). All subtypes of breast cancer cell lines examined displayed aberrant DNA synthesis/Gap 2/mitosis progression and the basal-like and claudin-low cell lines exhibited increased percentages of chromatid cohesion defects. Furthermore, a decatenation Gap 2 checkpoint gene expression signature identified in the cell line panel correlated with clinical outcomes in breast cancer patients, suggesting that breast tumors may also harbor defects in decatenation Gap 2 checkpoint function. Taken together, these data imply that pharmacological targeting of signaling pathways driving these phenotypes may lead to the development of novel personalized treatment strategies for the latter two subtypes which currently lack targeted therapeutic options because of their triple negative breast cancer status.

Lipin-1 regulation of phospholipid synthesis maintains endoplasmic reticulum homeostasis and is critical for triple-negative breast cancer cell survival.

Cancer cells reprogram their metabolism to increase the synthesis of macromolecules for rapid proliferation. Compared to fatty acids, much less is known about the synthesis of phospholipids, which is essential for membrane biogenesis in cancer cells. We found that LPIN1, which encodes lipin-1, a phosphatidic acid phosphatase (PAP) controlling the rate-limiting step in the phospholipid synthesis pathway, is highly up-regulated in basal-like triple-negative breast cancer (TNBC). Moreover, high LPIN1 expression correlates with the poor prognosis of these patients. Knockdown of LPIN1 increases apoptosis in basal-like TNBC cell lines, whereas it has minimal or less effect on normal human mammary gland epithelial cells (HMECs) and estrogen receptor-positive breast cancer cell lines. Fatty acid incorporation and lipidomics analyses showed that LPIN1 knockdown blocks phospholipid synthesis and changes membrane lipid compositions that ultimately induce the activation of 1 of the 3 branches of unfolded protein responses, the inositol-requiring enzyme-1α pathway. We also show for the first time, to our knowledge, that lipin-1 knockdown significantly inhibits tumor growth in vivo using an orthotopic xenograft breast mouse model. Our results suggest that lipin-1 is a potential target for cancer therapy.-He, J., Zhang, F., Tay, L. W. R., Boroda, S., Nian, W., Levental, K. R., Levental, I., Harris, T. E., Chang, J. T., Du, G. Lipin-1 regulation of phospholipid synthesis maintains endoplasmic reticulum homeostasis and is critical for triple-negative breast cancer cell survival.

Acetylated a-tubulin sense the change of extracellular matrix to regulate the invasion and metastasis of breast cancer

Objective To reveal acetylated a-tubulin acts as pressure sensors, sensing the changes in extracellular matrix to impact on the invasion and metastasis of breast cancer. Methods The acetylated alpha microtubule protein expressions were detected, and its relationship with invasion and metastasis in breast cancer clinical specimens and different molecular subtypes of breast cancer cell lines were analyzed. The expression of acetylated a-tubulin was interfered through chemical methods, and cell morphology and the change of the invasion and metastasis ability were detected under the condition of different matrix hardness. Results The expression of acetylated a-tubulin was highest in basal-like breast cancer tissue and cell lines, and was lowest expressed in the luminal B breast cancer tissue and the breast cancer cell lines. The expression of acetylated a-microtubule was positively correlated with the occurrence of breast cancer. Under the condition of soft substrate cultivation, cell polarization was declined, becoming the circular or oval shape. The acetylated a-tubulin caused reduction in cell polarity, accompanied with less invasion and metastasis ability. Conclusions The acetylated a-tubulin acts as pressure sensors, sensing the sclerosis of extracellular matrix in the process of tumorigenesis, promoting invasion and metastasis of breast cancer. Key words: Tubulin/ME; Extracellular matrix/ME; Breast neoplasms; Neoplasm invasiveness; Neoplasm metastasis

Abstract P3-07-08: Molecular subtype-specific expression of long noncoding RNA regulates proliferation of basal-like breast cancer cells

Abstract Background: Basal-like breast cancer (BLBC) disproportionally affects younger women and African American women, displaying aggressive clinical behavior with poor outcomes. BLBC is difficult to treat due to its lack of defined molecular targets, and with current treatment, patients often develop metastatic disease. A growing body of evidence points to long noncoding (lnc) RNAs as mediators of tumor progression, suggesting a new class of targets in cancer therapy. While dynamic changes in lncRNA expression are observed across many types of cancer, our understanding of their role in cancer biology is limited. The aim of this study is to identify lncRNAs differentially expressed in BLBC and to characterize the functional features of candidate lncRNA. Methods: Breast tumors and normal breast tissues were recruited from the U of Chicago Breast Cancer Tissue Bank under IRB approved protocols. Microarray profiling was done using Human LncRNA Array v3 (Arraystar) containing 30,586 lncRNAs and 26,109 mRNAs. Non-poly(A) RNAs were included with ribo-zero RNA-seq (Illumina HiSeq 4000). Molecular subtype of breast tumors was determined by PAM50 intrinsic classifier. In addition, CpG methylation of lncRNA promoter regions was analyzed with TCGA HumanMethylation450 Array data from 588 breast tissues. We performed in vitro studies using antisense oligonucleotide (ASO) knockdown and CRISPR-on overexpression in BLBC cell lines. Phenotypic consequences of perturbations of specific lncRNA expression were assessed using proliferation, apoptosis, cell cycle and homologous recombination assays. Results: Microarray profiling of breast tissues from 30 African American women revealed a unique lncRNA signature in basal-like tumors compared to non-basal like tumors. Hundreds of lncRNAs were specifically expressed in BLBC, with >100-fold differences in some lncRNAs compared to tumors from other subtypes or normal breast tissues. Through statistical and in silico analyses we selected lncRNAs displaying increased expression in basal-like tumors (vs non-basal tumors) and BLBC cell lines (vs non-basal cell lines) with a trend of higher expression in cells isolated from women of African ancestry for functional studies. RNA-seq of 50 additional breast tissues recapitulated the distinct lncRNA clustering within the basal-like subtype. TCGA analysis of CpG islands in several lncRNA promoter regions revealed hypo-methylation when compared to non-BLBC, signifying subtype specific epigenetic regulation. ASO knockdown of candidate lncRNAs significantly increased apoptosis and decreased proliferation while CRISPR-on overexpression decreased cell sensitivity to doxorubicin treatment. Depletion of specific lncRNAs caused an increased proportion of cells in G2 phase of the cell cycle, indicating that overexpression of particular lncRNAs may contribute to aberrant cell cycle progression. Cis and trans-regulation of gene expression by lncRNAs is currently under investigation through RNA immunoprecipitation and genome-wide gene expression profiling. Conclusion: We propose that subtype specific lncRNAs function as onco-RNAs specific to BLBC, driving cellular proliferation and increasing resistance to DNA damaging chemotherapies through regulation of the cell cycle. Citation Format: Boatman SM, Han Y-J, Zhang J, Zheng Y, Yeh AC, Olopade OI. Molecular subtype-specific expression of long noncoding RNA regulates proliferation of basal-like breast cancer cells [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-07-08.

Knockdown of CAVEOLIN-1 Sensitizes Human Basal-Like Triple-Negative Breast Cancer Cells to Radiation

Background/Aims: Triple-negative breast cancer (TNBC) is a high-risk breast cancer phenotype without specific targeted therapy options and is significantly associated with increased local recurrence in patients treated with radiotherapy. CAVEOLIN-1 (CAV-1)-mediated epidermal growth factor receptor (EGFR) nuclear translocation following irradiation promotes DNA repair and thus induces radiation resistance. In this study, we aimed to determine whether knockdown of CAV-1 enhances the radiosensitivity of basal-like TNBC cell lines and to explore the possible mechanisms. Methods: Western blotting was used to compare protein expression in a panel of breast cancer cell lines. Nuclear accumulation of EGFR as well as DNA repair and damage at multiple time points following irradiation with or without CAV-1 siRNA pretreatment were investigated using western blotting and confocal microscopy. The radiosensitizing effect of CAV-1 siRNA was evaluated using a clonogenic assay. Flowcytometry was performed to analyse cell apoptosis and cell cycle alteration. Results: We found that CAV-1 is over-expressed in basal-like TNBC cell lines and barely expressed in HER-2-positive cells; additionally, we observed that HER-2-positive cell lines are more sensitive to irradiation than basal-like TNBC cells. Our findings revealed that radiation-induced EGFR nuclear translocation was impaired by knockdown of CAV-1. In parallel, radiation-induced elevation of DNA repair proteins was also hampered by pretreatment with CAV-1 siRNA before irradiation. Silencing of CAV-1 also promoted DNA damage 24 h after irradiation. Colony formation assays verified that cells could be radiosensitized after knockdown of CAV-1. Furthermore, G₂/M cell cycle arrest and apoptosis enhancement may also contribute to the radiosensitizing effect of CAV-1 siRNA. Conclusion: Our results support the hypothesis that CAV-1 knockdown by siRNA causes increased radiosensitivity in basal-like TNBC cells. The mechanisms associated with this effect are reduced DNA repair through delayed CAV-1-associated EGFR nuclear accumulation and induction of G₂/M arrest and apoptosis through the combined effects of CAV-1 siRNA and radiation.

FBP1 modulates cell metabolism of breast cancer cells by inhibiting the expression of HIF-1α.

This study aimed to investigate the function of fructose-1, 6-bisphosphatase 1 (FBP1) in regulating cell growth and metabolism through hypoxia-inducible factor 1α (HIF-1α)-dependent hypoxic response in breast cancer cells. Two human breast carcinoma cell lines, including luminal-like cell line MCF-7 and basal-like cell line MDA-MB-468, were cultured under hypoxia condition, then the expressions of FBP1 and HIF-1α were detected by western blotting. In addition, up-regulated FPB1 in MDA-MB-468 cells were induced by lentivirus. Next, cell growth, migration and glucose metabolism were evaluated by MTT assay, Transwell and commercial kits, as well as the expressions of HIF-1α target genes, including pyruvate dehydrogenase kinase 1 (PDK1), lactate dehydrogenase A (LDHA), glucose transporter 1 (GLUT1) and vascular endothelial growth factor (VEGF) were detected by RT-qPCR. Furthermore, chromatin immunoprecipitation was used to estimate whether the hypoxia response elements (HREs) of PDK1, LDHA, GLUT1 and VEGF promoters were incorporated with FBP1. FBP1 was downregulated in MDA-MB-468 cells compared with MCF-7 cells. Overexpression of FBP1 in MDA-MB-468 cells reduced cell growth (p < 0.05) and migration (p < 0.05) as well as glycose consumption (p < 0.05) and lactate production (p < 0.05). In addition, overexpressed FBP1 inhibited HIF-1α protein expression and the mRNA levels of PDK1, LDHA, GLUT1 and VEGF (p < 0.05) under hypoxia condition. Also, FBP1 was revealed to have a concrete connection with PDK1. This study reveal that overexpressed FBP1 may repress tumor growth, migration and glycolysis via targeting HIF-1α in BLBC.

Genetic and Epigenetic Regulation of TOX3 Expression in Breast Cancer.

Genome wide association studies (GWAS) have identified low penetrance and high frequency single nucleotide polymorphisms (SNPs) that contribute to genetic susceptibility of breast cancer. The SNPs at 16q12, close to the TOX3 and CASC16 genes, represent one of the susceptibility loci identified by GWAS, showing strong evidence for breast cancer association across various populations. To examine molecular mechanisms of TOX3 regulation in breast cancer, we investigated both genetic and epigenetic factors using cell lines and datasets derived from primary breast tumors available through The Cancer Genome Atlas (TCGA). TOX3 expression is highly up-regulated in luminal subtype tumors compared to normal breast tissues or basal-like tumors. Expression quantitative trait loci (eQTL) analyses revealed significant associations of rs3803662 and rs4784227 genotypes with TOX3 expression in breast tumors. Bisulfite sequencing of four CpG islands in the TOX3 promoter showed a clear difference between luminal and basal-like cancer cell lines. 5-Aza-2’-deoxycytidine treatment of a basal-like cancer cell line increased expression of TOX3. TCGA dataset verified significantly lower levels of methylation of the promoter in luminal breast tumors with an inverse correlation between methylation and expression of TOX3. Methylation QTL (mQTL) analyses showed a weak or no correlation of rs3803662 or rs4784227 with TOX3 promoter methylation in breast tumors, indicating an independent relationship between the genetic and epigenetic events. These data suggest a complex system of TOX3 regulation in breast tumors, driven by germline variants and somatic epigenetic modifications in a subtype specific manner.

The Ribonucleic Complex HuR-MALAT1 Represses CD133 Expression and Suppresses Epithelial-Mesenchymal Transition in Breast Cancer.

Epithelial-to-mesenchymal transition (EMT) is a core process underlying cell movement during embryonic development and morphogenesis. Cancer cells hijack this developmental program to execute a multi-step cascade, leading to tumorigenesis and metastasis. CD133 (PROM1), a marker of cancer stem cells, has been shown to facilitate EMT in various cancers, but the regulatory networks controlling CD133 gene expression and function in cancer remain incompletely delineated. In this study, we show that a ribonucleoprotein complex including the long noncoding RNA MALAT1 and the RNA-binding protein HuR (ELAVL1) binds the CD133 promoter region to regulate its expression. In luminal nonmetastatic MCF-7 breast cancer cells, HuR silencing was sufficient to upregulate N-cadherin (CDH2) and CD133 along with a migratory and mesenchymal-like phenotype. Furthermore, we found that in the basal-like metastatic cell line MDA-MB-231 and primary triple-negative breast cancer tumor cells, the repressor complex was absent from the CD133-regulatory region, but was present in the MCF-7 and primary ER+ tumor cells. The absence of the complex from basal-like cells was attributed to diminished expression of MALAT1, which, when overexpressed, dampened CD133 levels. In conclusion, our findings suggest that the failure of a repressive complex to form or stabilize in breast cancer promotes CD133 upregulation and an EMT-like program, providing new mechanistic insights underlying the control of prometastatic processes. Cancer Res; 76(9); 2626-36. ©2016 AACR.

Abstract 4207: Secreted proteins from breast cancer cell lines as a source of cancer biomarkers

Abstract Introduction: Breast cancer is a heterogeneous disease whose molecular diversity is not well reflected in clinical and microscopic markers used for prognostic information and treatment decisions. Traditionally, most biomarkers are based on tissue samples. To increase efficiency, precise liquid biopsies are needed to detect breast cancer at an early stage including its molecular phenotype, to monitor disease progression, and to predict treatment response. Cell line secretomes are enriched with proteins already linked to tumorigenesis, many of which will be present in biological fluids. Methods: Here, we studied the secreted proteins in conditioned media (CM) from two basal-like (HS-578, MB-231) and two luminal-like breast cancer cell lines (MCF-7, BT-474), using liquid chromatography-tandem mass spectrometry. The resulting data were analyzed using SearchGUI, PeptideShaker, Progenesis software and DAVID. Results: In total, 954 proteins were identified, of which 93 significantly differentially abundant (P-value ≤ 0.05 Mann-Whitney U, two or more peptides quantified) in the CM between basal-like and luminal-like cell lines. 76 proteins were more abundant in the CM from basal-like cell lines, including several proteins related to angiogenesis and extra-cellular matrix remodeling. Conclusion: This study shows the potential for using the secretome of breast cancer cell lines combined with mass-spectrometry for biomarker discovery. Citation Format: Even Birkeland, Monica Mannelqvist, Lars Andreas Akslen. Secreted proteins from breast cancer cell lines as a source of cancer biomarkers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4207. doi:10.1158/1538-7445.AM2015-4207

Abstract 725: Restoration of miR-100 sensitizes luminal A breast cancer to paclitaxel treatment by targeting mTOR

Abstract Based on molecular profiling, immunohistochemical detection of ERα, PR and Her2, and morphological evaluation, breast cancer is classified into five subtypes: Luminal A, Luminal B, Her2, Basal-like, and Normal-like. Each subtype has distinct prognosis and treatment response. The luminal A subtype nicely responds to endocrine therapy with a good prognosis, but is less responsive to chemotherapies including paclitaxel. According to a previous study, patients with luminal A breast cancer do not benefit from the addition of paclitaxel to their chemotherapies, but the underlying mechanisms are still not clear. We found that the expression of miRNA miR-100 is dramatically lower in luminal breast cancer cell lines compared to the basal-like subtype. In human breast cancer specimens, while miR-100 expression was downregulated when compared to the matched normal breast tissues, the downregulation in luminal A subtype tumors was more dramatic when compared to other subtypes. We therefore propose that lower levels of miR-100 expression could be responsible for decreased sensitivity of luminal A breast cancer to paclitaxel. To test this hypothesis, we expressed miR-100 in the MCF-7 luminal A breast cancer cell line, and found that expression of miR-100 sensitized MCF-7 cells to paclitaxel treatment by promoting paclitaxel-induced apoptosis and cell cycle arrest. We also suppressed miR-100 expression in the MDA-MB-231 basal-like cell line, and found that miR-100 downregulation desensitized MDA-MB-231 cells to paclitaxel. Tumorigenesis experiments in nude mice further support a role of miR-100 in luminal breast cancer's response to paclitaxel treatment. mTOR, an important player in the PI3K/mTOR signaling pathway, has been identified as a downstream target of miR-100, and combination of rapamycin, a mTOR inhibitor, with paclitaxel enhances the effect of chemotherapy in breast cancer. We found that miR-100 expression inhibited mTOR expression in MCF-7 cells, while suppression of miR-100 increased mTOR expression in MDA-MB-231 cells. These results suggest that miR-100 sensitizes luminal A breast cancer cells to paclitaxel via targeting mTOR. They also provide an explanation for the resistance of luminal A breast cancer to paclitaxel treatment. Citation Format: Baotong Zhang, Ranran Zhao, Yuan He, Xing Fu, Jin-Tang Dong. Restoration of miR-100 sensitizes luminal A breast cancer to paclitaxel treatment by targeting mTOR. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 725. doi:10.1158/1538-7445.AM2015-725

Systematic Mapping of Kinase Addiction Combinations in Breast Cancer Cells by Integrating Drug Sensitivity and Selectivity Profiles

Chemical perturbation screens offer the possibility toidentify actionable sets of cancer-specific vulnerabilities. However, most inhibitors of kinases or othercancer targets result in polypharmacological effects,which complicate the identification of target dependencies directly from the drug-response phenotypes. In this study, we developed a chemical systems biology approach that integrates comprehensive drug sensitivity and selectivity profiling to provide functional insights into both single and multi-target oncogenic signal addictions. When applied to 21 breast cancer cell lines, perturbed with 40 kinase inhibitors, the subtype-specific addiction patterns clustered in agreement with patient-derived subtypes, while showing considerable variability between the heterogeneous breast cancers. Experimental validation of the top predictions revealed a number of co-dependencies between kinase targets that led to unexpected synergistic combinations between their inhibitors, such as dasatinib and axitinib in the triple-negative basal-like HCC1937 cell line.

Abstract A35: Proteomic and transcriptional profiling reveal differential responses to combined MEK and PI3K-mTOR network inhibition in basal-like and mesenchymal subtypes of triple negative breast cancer

Abstract Background: Activated MAPK and PI3K/AKT/mTOR pathway signaling are associated with poor prognosis in triple negative Breast cancer (TNBC). Therefore, suppression of both arms of the MAPK/PI3K/AKT/mTOR network is a promising strategy for targeting TNBC. Here we explore the anti-tumor effects of combinations of MEK inhibitor with PI3K, AKT, or mTOR inhibitors with a focus on cell fate and biomarker development in two major subtypes of TNBC, basal-like and mesenchymal. Methods: Combinations of a MEK inhibitor with a PI3K inhibitor, AKT inhibitor, dual mTORC 1/2 inhibitor, or rapalog were evaluated in TNBC cell lines and an orthotopically implanted patient-derived xenograft (PDX) model of TNBC. We utilized reverse-phase protein array (RPPA) and quantitative real-time PCR to interrogate the signaling architecture and transcriptional activity of the treated cell lines. Results: All combinations synergistically suppress the growth of basal-like and mesenchymal TNBC models. RPPA confirms that all combinations suppress common network targets including pERK Th202/T204, pPRAS40 T246, pS6rp S235/236, and p4E-BP1 S65 in all cell lines. Notably, however, comparable repression of MAPK/PI3K/AKT/mTOR signaling produces distinct fates in basal-like and mesenchymal subtypes. Basal-like cell lines preferentially undergo delayed cell death with surviving cells displaying profound growth arrest. In contrast, mesenchymal cell lines respond with uniform quiescence exhibiting little or no cell death. Transcriptional analysis corroborates these phenotypic effects demonstrating differential modulation of genes regulating apoptosis and proliferation in basal-like versus mesenchymal cell lines. Drug treated mesenchymal cells exhibit transcriptional ‘reprogramming’ of epithelial-mesenchymal status as evidenced by reduced mesenchymal gene expression inferring potential effects on invasion and metastasis. In a PDX model of basal-like TNBC that is paclitaxel resistant, early and sustained suppression of tumor growth was achieved by treating once daily with the MEK inhibitor, GDC-0973, in combination with either the PI3K inhibitor, GDC-0941, or the rapalog, Temsirolimus. Concurrent dosing on this intense schedule was associated with some toxicity that could likely be diminished with dose modifications. Conclusions: These data highlight the therapeutic potential of combined MEK and PI3K/AKT/mTOR inhibition in chemo-resistant TNBC. Importantly, they demonstrate innate differences in the response of basal-like and mesenchymal subtypes of TNBC to these combinations, supporting the concept that molecular subtype will be an important predictor of response both in this setting and for other targeted therapies. The combination of GDC-0973 and GDC-0941 performed particularly well in a taxane resistant PDX model and deserves further evaluation in clinical trials for the treatment of TNBC. Citation Format: Sarah J. Schweber, Alicia Rodriguez-Gabin, Jinghang Zhang, Valerie Calvert, Huiping Liu, Emanuel M. Petricoin, III, Eleni Andreopoulou, Susan Band Horwitz, Hayley M. McDaid. Proteomic and transcriptional profiling reveal differential responses to combined MEK and PI3K-mTOR network inhibition in basal-like and mesenchymal subtypes of triple negative breast cancer. [abstract]. In: Proceedings of the AACR Special Conference: Targeting the PI3K-mTOR Network in Cancer; Sep 14-17, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(7 Suppl):Abstract nr A35.

Targeting Mdmx to treat breast cancers with wild-type p53.

The function of the tumor suppressor p53 is universally compromised in cancers. It is the most frequently mutated gene in human cancers (reviewed). In cases where p53 is not mutated, alternative regulatory pathways inactivate its tumor suppressive functions. This is primarily achieved through elevation in the expression of the key inhibitors of p53: Mdm2 or Mdmx (also called Mdm4) (reviewed). In breast cancer (BrCa), the frequency of p53 mutations varies markedly between the different subtypes, with basal-like BrCas bearing a high frequency of p53 mutations, whereas luminal BrCas generally express wild-type (wt) p53. Here we show that Mdmx is unexpectedly highly expressed in normal breast epithelial cells and its expression is further elevated in most luminal BrCas, whereas p53 expression is generally low, consistent with wt p53 status. Inducible knockdown (KD) of Mdmx in luminal BrCa MCF-7 cells impedes the growth of these cells in culture, in a p53-dependent manner. Importantly, KD of Mdmx in orthotopic xenograft transplants resulted in growth inhibition associated with prolonged survival, both in a preventative model and also in a treatment model. Growth impediment in response to Mdmx KD was associated with cellular senescence. The growth inhibitory capacity of Mdmx KD was recapitulated in an additional luminal BrCa cell line MPE600, which expresses wt p53. Further, the growth inhibitory capacity of Mdmx KD was also demonstrated in the wt p53 basal-like cell line SKBR7 line. These results identify Mdmx growth dependency in wt p53 expressing BrCas, across a range of subtypes. Based on our findings, we propose that Mdmx targeting is an attractive strategy for treating BrCas harboring wt p53.

Targeting CD151 by lentivirus-mediated RNA interference inhibits luminal and basal-like breast cancer cell growth and invasion.

CD151 is a member of the tetraspanin family, which is involved in diverse cellular processes, including proliferation, motility, and invasion. However, the role of CD151 in breast cancer especially luminal and basal-like subtype breast cancer remains obscure. Here, we report the role of CD151 in the biological behaviors of luminal and basal-like subtype cell lines and the underlying molecular mechanism. A eukaryotic expression vector expressing both CD151 shRNA and GFP was transfected into MCF-7 and MDA-MB-468 cells. The CD151 gene-silencing effect is authenticated by real-time PCR and Western blot. Our data show that the capacity for proliferation, migration, and invasion of two kinds of cells is diminished after Knockdown of CD151 via lentivirus-mediated CD151 specific shRNA. Tumor cells are arrested in G0/G1 phase. Apoptosis is increased. Moreover, we also demonstrate that the expressions of mmp26 and CD147 are inhibited by knockdown of CD151. But the inhibition depends on the cell type. We can conclude that silencing gene CD151 inhibits expression of properties that are associated with the malignant phenotype of MCF-7 and MDA-MB-468 cells. It may become a potential target in breast cancer therapy especially for luminal and basal subtypes.