Gene Expression-Based Outcome For Breast Cancer Online Research Articles

The PTX3/TLR4 autocrine loop as a novel therapeutic target in triple negative breast cancer

BackgroundThe pattern recognition receptor long pentraxin-3 (PTX3) plays conflicting roles in cancer by acting as an oncosuppressor or as a pro-tumor mediator depending on tumor context. Triple negative breast cancer (TNBC) represents the most aggressive histotype of breast cancer, characterized by the lack of efficacious therapeutic targets/approaches and poor prognosis. Thus, the characterization of new molecular pathways and/or alternative druggable targets is of great interest in TNBC.MethodsThe expression of PTX3 in BC tumor samples and in BC cell lines has been analyzed using the Gene Expression-Based Outcome for Breast Cancer Online (GOBO), qPCR, Western blot and ELISA assay. The contribution of tumor and stromal cells to PTX3 production in TNBC was assessed by analyzing single cell RNA sequencing data and RNAscope performed on TNBC tumor samples. In order to investigate the effects of PTX3 in TNBC, different cell lines were engineered to knock-down (MDA-MB-231 and BT549 cells) or overexpress (MDA-MB-468 and E0771 cells) PTX3. Finally, using these engineered cells, in vitro (including gene expression profiling and gene set enrichment analyses) and in vivo (orthotopic tumor models in immune-compromised and immune competent mice) analyses were performed to assess the role and the molecular mechanism(s) exerted by PTX3 in TNBC.ResultsIn silico and experimental data indicate that PTX3 is mainly produced by tumor cells in TNBC and that its expression levels correlate with tumor stage. Accordingly, gene expression and in vitro results demonstrate that PTX3 overexpression confers a high aggressive/proliferative phenotype and fosters stem-like features in TNBC cells. Also, PTX3 expression induces a more tumorigenic potential when TNBC cells are grafted orthotopically in vivo. Conversely, PTX3 downregulation results in a less aggressive behavior of TNBC cells. Mechanistically, our data reveal that PTX3 drives the activation of the pro-tumorigenic Toll-like receptor 4 (TLR4) signaling pathway in TNBC, demonstrating for the first time that the PTX3/TLR4 autocrine stimulation loop contributes to TNBC aggressiveness and that TLR4 inhibition significantly impacts the growth of PTX3-producing TNBC cells.ConclusionAltogether, these data shed light on the role of tumor-produced PTX3 in TNBC and uncover the importance of the PTX3/TLR4 axis for therapeutic and prognostic exploitation in TNBC.Graphical abstract

A matrisome RNA signature from early-pregnancy mouse mammary fibroblasts predicts distant metastasis-free breast cancer survival in humans

BackgroundDuring pregnancy, the mouse mammary ductal epithelium branches and grows into the surrounding stroma, requiring extensive extracellular matrix (ECM) and tissue remodelling. It therefore shows parallels to cancer invasion. We hypothesised that similar molecular mechanisms may be utilised in both processes, and that assessment of the stromal changes during pregnancy-associated branching may depict the stromal involvement during human breast cancer progression.MethodsImmunohistochemistry (IHC) was employed to assess the alterations within the mouse mammary gland extracellular matrix during early pregnancy when lateral branching of the primary ductal epithelium is initiated. Primary mouse mammary fibroblasts from three-day pregnant and age-matched non-pregnant control mice, respectively, were 3D co-cultured with mammary epithelial cells to assess differences in their abilities to induce branching morphogenesis in vitro. Transcriptome analysis was performed to identify the underlying molecular changes. A signature of the human orthologues of the differentially expressed matrisome RNAs was analysed by Kaplan–Meier and multi-variate analysis in two large breast cancer RNA datasets (Gene expression-based Outcome for Breast cancer Online (GOBO) und Kaplan–Meier Plotter), respectively, to test for similarities in expression between early-pregnancy mouse mammary gland development and breast cancer progression.ResultsThe ECM surrounding the primary ductal network showed significant differences in collagen and basement membrane protein distribution early during pregnancy. Pregnancy-associated fibroblasts (PAFs) significantly enhanced branching initiation compared to age-matched control fibroblast. A combined signature of 64 differentially expressed RNAs, encoding matrisome proteins, was a strong prognostic indicator of distant metastasis-free survival (DMFS) independent of other clinical parameters. The prognostic power could be significantly strengthened by using only a subset of 18 RNAs (LogRank P ≤ 1.00e−13; Hazard ratio (HR) = 2.42 (1.8–3.26); p = 5.61e−09). The prognostic power was confirmed in a second breast cancer dataset, as well as in datasets from ovarian and lung cancer patients.ConclusionsOur results describe for the first time the early stromal changes that accompany pregnancy-associated branching morphogenesis in mice, specify the early pregnancy-associated molecular alterations in mouse mammary fibroblasts, and identify a matrisome signature as a strong prognostic indicator of human breast cancer progression, with particular strength in oestrogen receptor (ER)-negative breast cancers.

Comprehensive analysis of genomic alterations, clinical outcomes, putative functions and potential therapeutic value of MMP11 in human breast cancer

The aim of the current study is to comprehend the prognostic and therapeutic value of matrix metalloproteinase (MMP11) in breast cancer using computational analyses. Gene expression-based Outcome for Breast cancer Online (GOBO) analysis revealed that MMP11 expression was increased in tumor when compared to normal. Among the subtypes, human epidermal growth factor receptor 2 (HER2) enriched and estrogen receptor (ER) positive showed higher expression of MMP11. The results were independently validated with cBioPortal and Oncomine databases. Tumors with high MMP11 expression showed poor overall survival and distant metastasis free survival. Further, protein-protein interactome network was constructed and molecular pathway analysis using Reactome database identified its putative role in diverse cellular processes. In addition, UALCAN web portal revealed hypomethylation in the promoter region of MMP11 in breast tumors. Molecular docking using iGEMDOCK and Autodock Vina were performed to identify natural compounds and repurposed drugs interaction with MMP11. Our study confirms the prognostic significance of MMP11 in breast cancer and their intrinsic subtypes. Twelve bio-compounds which were predominantly flavonoids and anti-psychotic drug pimozide showed significant docking scores with MMP11. Further, potential of these compounds in inhibiting MMP11 related molecular pathways and in targeting breast cancer cells are yet to be studied.

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases.

In recent years, emerging databases were designed to lower the barriers for approaching the intricate cancer genomic datasets, thereby, facilitating investigators to analyze and interpret genes, samples and clinical data across different types of cancer. Herein, we describe a practical operation procedure, taking ID1 (Inhibitor of DNA binding proteins 1) as an example, to characterize the expression patterns of biomarker and survival predictors of breast cancer based on pooled clinical datasets derived from online accessible databases, including ONCOMINE, bcGenExMiner v4.0 (Breast cancer gene-expression miner v4.0), GOBO (Gene expression-based Outcome for Breast cancer Online), HPA (The human protein atlas), and Kaplan-Meier plotter. The analysis began with querying the expression pattern of the gene of interest (e.g., ID1) in cancerous samples vs. normal samples. Then, the correlation analysis between ID1 and clinicopathological characteristics in breast cancer was performed. Next, the expression profiles of ID1 was stratified according to different subgroups. Finally, the association between ID1 expression and survival outcome was analyzed. The operation procedure simplifies the concept to integrate multidimensional data types at the gene level from different databases and test hypotheses regarding recurrence and genomic context of gene alteration events in breast cancer. This method can improve the credibility and representativeness of the conclusions, thereby, present informative perspective on a gene of interest.

Silencing Y-box binding protein-1 inhibits triple-negative breast cancer cell invasiveness via regulation of MMP1 and beta-catenin expression.

Y-box binding protein-1 (YB-1), an important transcription and translation regulator protein, is known to increase cancer cell invasiveness and spreading. Here, we report its role in breast cancer, particularly in mediating cell invasion in triple-negative breast cancer (TNBC). YB-1 stable knockdown (shYB-1) significantly reduced the invasive potential of MDA-MB-231 TNBC cells in 2D and 3D (spheroid) cultures. Whole proteome mass spectrometry analysis showed an enrichment of cell adhesion and cell to matrix interaction proteins, notably, matrix metalloproteinase-1 (MMP1) and beta-catenin (CTNNB1), which are known to play critical roles in cancer metastasis. shYB-1 cells exhibited substantial downregulation of MMP1 and CTNNB1 mRNA and protein expression, with reduced MMP1 enzyme activity. YB-1 was also observed to bind to the promoter of MMP1 and overexpression of MMP1 plasmid in shYB-1 cells increased cell invasion. Finally, analysis of tumour samples from the Gene Expression-Based Outcome for Breast Cancer Online (GOBO) database revealed that high gene expressions of YBX1, MMP1 and CTNNB1 predict for a significantly lower 10-year distant metastasis free survival. Altogether, this study shows that YB-1 mediates breast cancer invasion and metastasis via regulation of MMP1 and beta-catenin.

A-kinase anchor protein 12 (AKAP12) inhibits cell migration in breast cancer

A-kinase anchor protein 12 (AKAP12) also known as Gravin and SSeCKS, is a novel potent scaffold protein for many key signaling factors, such as protein kinase C (PKC), PKA, cyclins as well as F-actin. AKAP12 expression is known to be suppressed in several human malignancies including breast, prostate, gastric and colon cancers. In this study, we evaluated the role of AKAP12 in the migration of breast cancer cells, an important cellular process in cancer progression. AKAP12 gene expression was analyzed in human breast cancer tissues using the Gene expression-based Outcome for Breast cancer Online (GOBO) database and TissueScan array, followed by relapse free survival (RFS) analysis with the Kaplan-Meier Plotter. AKAP12 protein was then analyzed in normal MCF10A breast cell line and six different breast cancer cell lines (AU565, Hs578T, MCF7, MDA-MB-231, T47D and ZR751). After which, siRNA-mediated knockdown of AKAP12 was carried out in MCF10A, MDA-MB-231 and Hs578T cells, followed by phenotypic assays. AKAP12 was observed to be reduced in breast cancer tissues as analyzed by GOBO and TissueScan array. Kaplan Meier survival analysis revealed that patients with AKAP12 gene expression had a higher RFS survival. There was also decreased AKAP12 protein expression in breast cancer cell lines compared to MCF10A normal epithelial breast cell line. Knockdown of AKAP12 in both MCF10A cells and Hs578T cells induced cell migration but did not alter cell proliferation. Moreover, siAKAP12 in aggressive MDA-MB-231 breast cancer cells led to an increase in cell migration. Immunofluorescence analysis of AKAP12 depleted MCF10A cells also revealed formation of thick stress fibers which could affect cell migration. Hence, the findings in this study suggest that AKAP12 is a potential metastasis suppressor in breast cancer.

Prognostic value of DKK2 from the Dickkopf family in human breast cancer.

Breast cancer is one of the most frequently diagnosed types of cancer with a high mortality and malignancy rate in women worldwide. The Dickkopf (DKK) protein family, as a canonical Wnt/β-catenin pathway antagonist, has been implicated in both physiological and pathological processes. This study aimed to comprehensively characterize the prognostic value and elucidate the mechanisms of DKKs in breast cancer and its subtypes. Firstly, DKK mRNA expression and corresponding outcome were analyzed by means of the Gene Expression-Based Outcome for Breast Cancer Online (GOBO) platform based on PAM50 intrinsic breast cancer subtypes. Subsequently, we extracted breast cancer datasets from the Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) to validate the expression profile and prognostic values from the GOBO platform. Moreover, a protein-protein network was created and functional enrichment was conducted to explore the underlying mechanisms of action of the DKKs. In addition, we uncovered the genetic and epigenetic alterations of DKK2 in breast cancer. The main finding of this study was the differential roles of DKKs in the PAM50 subtypes of breast cancer analyzed. The overall trend was that a high level of DKK2 was associated with a good survival in breast cancer, although it played an opposite role in the Normal-like subtype. We also found that DKK2 carried out its functions through multiple signaling pathways, not limited to the Wnt/β-catenin cascade in breast cancer. Finally, we used our own data to validate the bioinformatics analysis data for DKK2 by RT-qPCR. Taken together, our findings suggest that DKK2 may be a potential prognostic biomarker for the Normal-like subtype of breast cancer. However, the prognostic role of DKKs in the subtypes of breast cancer still requires validation by larger sample studies in the future.

Distinct expression of CDCA3, CDCA5, and CDCA8 leads to shorter relapse free survival in breast cancer patient.

Breast cancer is a dangerous disease that results in high mortality rates for cancer patients. Many methods have been developed for the treatment and prevention of this disease. Determining the expression patterns of certain target genes in specific subtypes of breast cancer is important for developing new therapies for breast cancer. In the present study, we performed a holistic approach to screening the mRNA expression of six members of the cell division cycle-associated gene family (CDCA) with a focus on breast cancer using the Oncomine and The Cancer Cell Line Encyclopedia (CCLE) databases. Furthermore, Gene Expression-Based Outcome for Breast Cancer Online (GOBO) was also used to deeply mine the expression of each CDCA gene in clinical breast cancer tissue and breast cancer cell lines. Finally, the mRNA expression of the CDCA genes as related to breast cancer patient survival were analyzed using a Kaplan-Meier plot. CDCA3, CDCA5, and CDCA8 mRNA expression levels were significantly higher than the control sample in both clinical tumor sample and cancer cell lines. These highly expressed genes in the tumors of breast cancer patients dramatically reduced patient survival. The interaction network of CDCA3, CDCA5, and CDCA8 with their co-expressed genes also revealed that CDCA3 expression was highly correlated with cell cycle related genes such as CCNB2, CDC20, CDKN3, and CCNB1. CDCA5 expression was correlated with BUB1 and TRIP13, while CDCA8 expression was correlated with BUB1 and CCNB1. Altogether, these findings suggested CDCA3, CDCA5, and CDCA8 could have a high potency as targeted breast cancer therapies.

DCYTB is a predictor of outcome in breast cancer that functions via iron-independent mechanisms

BackgroundDuodenal cytochrome b (DCYTB) is a ferrireductase that functions together with divalent metal transporter 1 (DMT1) to mediate dietary iron reduction and uptake in the duodenum. DCYTB is also a member of a 16-gene iron regulatory gene signature (IRGS) that predicts metastasis-free survival in breast cancer patients. To better understand the relationship between DCYTB and breast cancer, we explored in detail the prognostic significance and molecular function of DCYTB in breast cancer.MethodsThe prognostic significance of DCYTB expression was evaluated using publicly available microarray data. Signaling Pathway Impact Analysis (SPIA) of microarray data was used to identify potential novel functions of DCYTB. The role of DCYTB was assessed using immunohistochemistry and measurements of iron uptake, iron metabolism, and FAK signaling.ResultsHigh DCYTB expression was associated with prolonged survival in two large independent cohorts, together totaling 1610 patients (cohort #1, p = 1.6e-11, n = 741; cohort #2, p = 1.2e-05, n = 869; log-rank test) as well as in the Gene expression-based Outcome for Breast cancer Online (GOBO) cohort (p < 1.0e-05, n = 1379). High DCYTB expression was also associated with increased survival in homogeneously treated groups of patients who received either tamoxifen or chemotherapy. Immunohistochemistry revealed that DCYTB is localized on the plasma membrane of breast epithelial cells, and that expression is dramatically reduced in high-grade tumors. Surprisingly, neither overexpression nor knockdown of DCYTB affected levels of ferritin H, transferrin receptor, labile iron or total cellular iron in breast cancer cells. Because SPIA pathway analysis of patient microarray data revealed an association between DCYTB and the focal adhesion pathway, we examined the influence of DCYTB on FAK activation in breast cancer cells. These experiments reveal that DCYTB reduces adhesion and activation of focal adhesion kinase (FAK) and its adapter protein paxillin.ConclusionsDCYTB is an important predictor of outcome and is associated with response to therapy in breast cancer patients. DCYTB does not affect intracellular iron in breast cancer cells. Instead, DCYTB may retard cancer progression by reducing activation of FAK, a kinase that plays a central role in tumor cell adhesion and metastasis.

Abstract B08: Expression of noncoding RNAs on the DLK1-DIO1 locus in EMT and breast cancer

Abstract The DLK1-DIO3 locus contains three paternally expressed protein-coding genes and maternally expressed non-protein coding genes, including the lncRNA MEG3 and a cluster of 54 miRNA, making it one of the largest miRNA clusters in the genome. A recent study showed that the degree of activation of the maternally inherited homolog of this region was correlated with the pluripotency of stem cells. Also, the maternal ncRNAs from the DLK1-DIO3 locus are amongst the few regions in the transcriptome able to discriminate between induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs), thereby linking this locus to the maintenance of stem cell character. In humans DLK1-DIO3-derived ncRNAs have been linked to both progression and inhibition of cancer. The objective of this study was to analyze the expression profile of the DLK1-DIO3-derived ncRNAs and in particular the lncRNA MEG3 in breast epithelial progenitor cell lines (D492 and HMLE) with high degree of plasticity towards epithelial to mesenchymal transition (EMT) and cancer progression. D492M and HMLEmes are mesenchymal derivatives of D492 and HMLE, respectively. Total RNA and small RNA sequencing revealed marked upregulation of the maternally expressed lncRNAs and the miRNAs on the DLK1-DIO3 locus in D492M compared to D492. This miRNA-cluster along with the lncRNA MEG3 is expressed from the maternal inherited homolog. Allele specific expression analysis shows that the increased expression of MEG3 in D492M is not caused by loss of imprinting but increased expression of the already expressed allele. These ncRNAs are also upregulated in HMLEmes compared to HMLE, showing that these effects are not cell line specific. qPCR analysis of primary tissue shows that MEG3 expression is 8-15 fold higher in stromal cells than epithelial cells of the breast. These results indicate that the MEG3 upregulation and/or the maternally expressed miRNA cluster could be critical regulators/effectors in the EMT/mesenchymal phenotype. Data from the The Cancer Genome Atlas consistently shows positive correlation between the expression of Meg3 and the miRNAs located at the DLK1-DIO3 genomic region. We have characterized the main splice-forms of the MEG3 gene, expressed in D492 and D492M. Out of the 12 different splice-forms, splice-form 1 (NR_002766) was mostly responsible for increased expression in D492M. Since EMT has been linked to metastatic behavior of epithelial-originating cancers we measured the expression of MEG3 in a series of clinically well-defined breast tumors (N= 125). Survival analysis showed lower overall survival in patients with high MEG3 expression (P=0.01). Comparison with expression and survival data from the online GOBO (Gene Expression-Based Outcome for Breast Cancer Online) database confirmed our observed negative relationship between MEG3 expression and survival which was particularly evident in luminal B type tumors. MEG3 is also negatively correlated with distant metastasis-free survival of poorly differentiated (grade 3) tumors, suggesting that MEG3 expression may be a valid marker of EMT during tumorigenesis. Conclusions: ncRNAs are increasingly seen as intrinsic regulators of stemness, tissue morphogenesis and cancer progression. Our data indicates that the maternally expressed ncRNAs at the DLK1-DIO3 region could be regulators of EMT in breast cancer. Future works will aim at understanding the biological role of MEG3 and the miRNA-cluster in these processes. Citation Format: Bylgja Hilmarsdottir, Eirikur Briem, Jon Thor Bergthorsson, Thorarinn Gudjonsson, Magnus Karl Magnusson. Expression of noncoding RNAs on the DLK1-DIO1 locus in EMT and breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B08.

The circadian gene CRY2 is associated with breast cancer aggressiveness possibly via epigenomic modifications.

Although the role of core circadian gene cryptochrome 2 (CRY2) in breast tumorigenesis has been demonstrated, the correlations of CRY2 with clinical parameters in breast cancer patients and its involvement in epigenetic processes such as DNA methylation remain relatively unexplored. In the current study, we first queried the Oncomine database and the Gene Expression-Based Outcome for Breast Cancer Online (GOBO) database to identify associations between CRY2 expression levels and clinical parameters in breast cancer patients. We then silenced CRY2 in vitro and performed a genome-wide methylation array to determine the epigenetic impact of CRY2 silencing. The Ingenuity Pathway Analysis software was used to further explore the genes exhibiting altered methylation identified using the array. We found that CRY2 was frequently down-regulated in breast cancer tissue compared to adjacent normal tissue or breast tissue from healthy controls. Lower CRY2 expression was associated with estrogen receptor (ER)-negativity (P < 0.0001), higher tumor grade (P < 0.0001), and shorter overall survival time in breast cancer patients (HR = 1.44, 95 % confidence interval (CI) 1.09-1.91). Genome-wide methylation analysis showed that a total of 515 CpG sites were hypermethylated following CRY2 knockdown, while 730 sites were hypomethylated. The pathway analysis revealed several cancer-relevant networks with genes exhibiting significantly altered methylation following CRY2 silencing. These findings suggest that the core circadian gene CRY2 is associated with breast cancer progression and prognosis, and that knockdown of CRY2 causes the epigenetic dysregulation of genes involved in cancer-relevant pathways, which provide further evidence supporting a role of the circadian system in breast tumorigenesis.

Abstract PR04: The Six2 homeoprotein mediates breast cancer metastasis via repressing E-cadherin

Abstract Homeobox genes are master regulators of embryogenesis and it is widely known that misexpression of these transcription factors can lead to tumorigenesis/ metastasis. The Six1 homeoprotein has been implicated in tumor onset and metastasis of many different cancers, including breast cancer. However, little is known about whether related homeoproteins in the Six family can affect tumor onset or progression. Recent studies have shown that while Six1 knockdown dramatically decreases metastasis, knockdown cells that are capable of metastasizing have upregulated a related family member, Six2. Interestingly, Six2 regulates stem/ progenitor cell populations and maintains a mesenchymal progenitor phenotype in the developing kidney; however, the role of Six2 in breast cancer progression has not been explored. Here, we demonstrate for the first time that up-regulation of Six2 in breast cancer cells can promote metastasis in a mechanism that differs from its related family member, Six1. Knockdown (KD) of Six2 in 66cl4 mouse mammary carcinoma cells significantly decreases lung metastasis in an immune-competent orthotopic mouse model, as compared to control KD. In contrast to what is seen with Six1 KD in the same orthotopic mouse model, no significant inhibition of primary tumor size was observed with Six2 knockdown, suggesting that unlike Six1, the functions of Six2 may be confined to later stages of tumor progression. Overexpression of Six2 in the weakly metastatic 4TO7 mouse mammary carcinoma cell line led to changes in cell morphology, increased anchorage independent growth and significantly enhanced lung metastasis in an immune competent mouse model. Microarray analysis was performed to determine the mechanism by which Six2 mediates metastasis and the epithelial marker E-Cadherin, whose loss has been implicated in the metastatic potential of many cancers, was dramatically downregulated in the 4TO7-Six2 expressing cells. Importantly, restoration of E-cadherin expression reduced lung metastasis induced by Six2 and increased survival of the animals. We further determine that repression of E-cadherin by Six2 is mediated via multiple mechanisms. SIP1/Zeb2 (zinc finger E box binding homeobox2), an epithelial to mesenchymal transition (EMT) inducer, is increased in cells overexpressing Six2, and Zeb2 KD in these cells reverts E-cadherin expression back to the level as that observed in the control cells and importantly leads to a reduction in metastasis in vivo. In addition, we find that Six2 may also repress E-cadherin though an epigenetic mechanism, since repression of E-cadherin downstream of Six2 can be reversed by inhibiting DNA methylation. Finally, analysis of Six2 expression from public microarray datasets indicates that Six2 is increased in breast cancers compared to normal breast tissue and that high expression of SIX2 correlates with poor prognosis (distant metastasis free survival, overall survival and relapse free survival) in 1881 human breast tumors examined using the GOBO (Gene Expression-Based Outcome for Breast Cancer Online) database. Moreover, a reverse correlation of E-cadherin and Six2 in breast cancer datasets suggest that Six2 promotes loss of E-cadherin in human breast cancer. Together, these data demonstrate that Six2 is a specific regulator of the metastatic process, through regulating E-cadherin expression. This abstract is also presented as Poster B094. Citation Format: Chu-An Wang, Paul Jedlicka, Aik-Choon Tan, Catherine Pham, Vadym Zaberezhnvv, Heide Ford. The Six2 homeoprotein mediates breast cancer metastasis via repressing E-cadherin. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr PR04.

MicroRNA-Regulated Protein-Protein Interaction Networks and Their Functions in Breast Cancer

MicroRNAs, which are small endogenous RNA regulators, have been associated with various types of cancer. Breast cancer is a major health threat for women worldwide. Many miRNAs were reported to be associated with the progression and carcinogenesis of breast cancer. In this study, we aimed to discover novel breast cancer-related miRNAs and to elucidate their functions. First, we identified confident miRNA-target pairs by combining data from miRNA target prediction databases and expression profiles of miRNA and mRNA. Then, miRNA-regulated protein interaction networks (PINs) were constructed with confident pairs and known interaction data in the human protein reference database (HPRD). Finally, the functions of miRNA-regulated PINs were elucidated by functional enrichment analysis. From the results, we identified some previously reported breast cancer-related miRNAs and functions of the PINs, e.g., miR-125b, miR-125a, miR-21, and miR-497. Some novel miRNAs without known association to breast cancer were also found, and the putative functions of their PINs were also elucidated. These include miR-139 and miR-383. Furthermore, we validated our results by receiver operating characteristic (ROC) curve analysis using our miRNA expression profile data, gene expression-based outcome for breast cancer online (GOBO) survival analysis, and a literature search. Our results may provide new insights for research in breast cancer-associated miRNAs.

Abstract 2705: Novel functions of the homeoprotein SIX2 in mediating anchorage independence and metastasis in breast cancer.

Abstract Homeobox genes encode for transcription factors that are master regulators of embryogenesis, and their misexpression has been implicated in multiple cancers. The role of the homeoprotein Six2 in developing kidney has been well demonstrated; however, its role in cancer progression is largely unknown. Here, we demonstrate, for the first time, that Six2 is causally involved in mammary tumor progression. When Six2 is knocked down (KD) in the 66cl4 mammary carcinoma cells, lung metastasis is significantly decreased compared to control KD; however, Six2 KD conferred no significant effect on growth of the primary tumor or on tumor-associated angiogenesis/lymphangiogenesis, in contrast to its closely related family member, Six1, which has been implicated in all the aforementioned properties; suggesting that Six2 may participate in later stages of the metastatic cascade. Expression of Six2 in the 4TO7 mammary carcinoma cell line (a cell line that is syngeneic with 66cl4, but expresses very low levels of endogenous Six2) led to changes in cell morphology, increased growth in soft agar, increased resistance to anoikis, and significantly enhanced lung metastasis in Balb/c mice. To determine the mechanism by which Six2 mediates metastasis, microarray analysis was performed on 4TO7-control and Six2 expressing cells. Interestingly, genes which have been implicated in lung metastasis (MMP, ANGPTL4, VCAM1) are significantly up-regulated in Six2 overexpressing 4TO7 cells; while the epithelial marker, E-Cadherin, is dramatically decreased. Finally, analysis of SIX2 expression from public microarray datasets indicates that SIX2 is increased in breast cancers compared to normal breast tissue. In addition, high expression of SIX2 correlates with poor prognosis (distant metastasis free survival, overall survival and relapse free survival) in 1881 human breast tumors examined using the GOBO (Gene Expression-Based Outcome for Breast Cancer Online) database, and upon further investigation we found that SIX2 expression is particularly associated with poor prognosis in luminal A, normal-like and ER-positive breast tumors. Together, our studies define a novel role of Six2 in breast cancer metastasis. Citation Format: Chu-An Wang, Paul Jedlicka, Vadym Zaberezhnyy, Aik-Choon Tan, Heide Ford. Novel functions of the homeoprotein SIX2 in mediating anchorage independence and metastasis in breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2705. doi:10.1158/1538-7445.AM2013-2705