Aylin Rizki

Polo-like Kinase 1 Is Involved in Invasion through Extracellular Matrix

Polo-like kinase 1 (PLK1) has important functions in maintaining genome stability via its role in mitosis. Because PLK1 is up-regulated in many invasive carcinomas, we asked whether it may also play a role in acquisition of invasiveness, a crucial step in transition to malignancy. In a model of metaplastic basal-like breast carcinoma progression, we found that PLK1 expression is necessary but not sufficient to induce invasiveness through laminin-rich extracellular matrix. PLK1 mediates invasion via vimentin and beta1 integrin, both of which are necessary. We observed that PLK1 phosphorylates vimentin on Ser82, which in turn regulates cell surface levels of beta1 integrin. We found PLK1 to be also highly expressed in preinvasive in situ carcinomas of the breast. These results support a role for the involvement of PLK1 in the invasion process and point to this pathway as a potential therapeutic target for preinvasive and invasive breast carcinoma treatment.

Simultaneous classification and relevant feature identification in high-dimensional spaces: application to molecular profiling data

Molecular profiling technologies monitor many thousands of transcripts, proteins, metabolites or other species concurrently in a biological sample of interest. Given such high-dimensional data for different types of samples, classification methods aim to assign specimens to known categories. Relevant feature identification methods seek to define a subset of molecules that differentiate the samples. This work describes LIKNON, a specific implementation of a statistical approach for creating a classifier and identifying a small number of relevant features simultaneously. Given two-class data, LIKNON estimates a sparse linear classifier by exploiting the simple and well-known property that minimising an L1 norm (via linear programming) yields a sparse hyperplane. It performs well when used for retrospective analysis of three cancer biology profiling data sets, (i) small, round, blue cell tumour transcript profiles from tumour biopsies and cell lines, (ii) sporadic breast carcinoma transcript profiles from patients with distant metastases < 5 years and those with no distant metastases ≥ 5 years and (iii) serum sample protein profiles from unaffected and ovarian cancer patients. Computationally, LIKNON is less demanding than the prevailing filter-wrapper strategy; this approach generates many feature subsets and equates relevant features with the subset yielding a classifier with the lowest generalisation error. Biologically, the results suggest a role for the cellular microenvironment in influencing disease outcome and its importance in developing clinical decision support systems.

Mesenchymal stem cells in mammary adipose tissue stimulate progression of breast cancer resembling the basal-type

Data are accumulating to support a role for adipose-derived mesenchymal stem cells (MSCs) in breast cancer progression; however, to date most studies have relied on adipose MSCs from non-breast sources. There is a particular need to investigate the role of adipose MSCs in the pathogenesis of basal-like breast cancer, which develops at a disproportionate rate in pre-menopausal African-American women with a gain in adiposity. The aim of this study was to better understand how breast adipose MSCs (bMSCs) contribute to the progression of basal-like breast cancers by relying on isogenic HMT-3255 S3 (pre-invasive) and T4-2 (invasive) human cells that upon transplantation into nude mice resemble this tumor subtype. In vitro results suggested that bMSCs may contribute to breast cancer progression in multiple ways. bMSCs readily penetrate extracellular matrix components in part through their expression of matrix metalloproteinases 1 and 3, promote the invasion of T4-2 cells and efficiently chemoattract endothelial cells via a bFGF-independent, VEGF-A-dependent manner. As mixed xenografts, bMSCs stimulated the growth, invasion and desmoplasia of T4-2 tumors, yet these resident stem cells showed no observable effect on the progression of pre-invasive S3 cells. While bMSCs form vessel-like structures within Matrigel both in vitro and in vivo and chemoattract endothelial cells, there appeared to be no difference between T4-2/bMSC mixed xenografts and T4-2 xenografts with regard to intra- or peri-tumoral vascularity. Collectively, our data suggest that bMSCs may contribute to the progression of basal-like breast cancers by stimulating growth and invasion but not vasculogenesis or angiogenesis.

Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features

BackgroundEnsemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins. The strategy exploits annotation data present in gene-centered corpora and utilizes ideas from statistical information retrieval to discover and characterize properties shared by subsets of the list. The practical utility of this method is demonstrated by employing it in a retrospective study of two non-overlapping sets of genes defined by a published investigation as markers for normal human breast luminal epithelial cells and myoepithelial cells.ResultsEach genetic locus was characterized using a finite set of biological properties and represented as a vector of features indicating attributes associated with the locus (a gene attribute profile). In this study, the vector space models for a pre-defined list of genes were constructed from the Gene Ontology (GO) terms and the Conserved Domain Database (CDD) protein domain terms assigned to the loci by the gene-centered corpus LocusLink. This data set of GO- and CDD-based gene attribute profiles, vectors of binary random variables, was used to estimate multiple finite mixture models and each ensuing model utilized to partition the profiles into clusters. The resultant partitionings were combined using a unanimous voting scheme to produce consensus clusters, sets of profiles that co-occured consistently in the same cluster. Attributes that were important in defining the genes assigned to a consensus cluster were identified. The clusters and their attributes were inspected to ascertain the GO and CDD terms most associated with subsets of genes and in conjunction with external knowledge such as chromosomal location, used to gain functional insights into human breast biology. The 52 luminal epithelial cell markers and 89 myoepithelial cell markers are disjoint sets of genes. Ensemble attribute profile clustering-based analysis indicated that both lists contained groups of genes with the functional properties of membrane receptor biology/signal transduction and nucleic acid binding/transcription. A subset of the luminal markers was associated with metabolic and oxidoreductase activities, whereas a subset of myoepithelial markers was associated with protein hydrolase activity.ConclusionGiven a set of genes and/or proteins associated with a phenomenon, process or system of interest, ensemble attribute profile clustering provides a simple method for collating and sythesizing the annotation data pertaining to them that are present in text-based, gene-centered corpora. The results provide information about properties common and unique to subsets of the list and hence insights into the biology of the problem under investigation.

42nd Annual Meeting of the American Society for Cell Biology, San Francisco, California, USA, 14-18 December 2002.

The Annual Meeting of the American Society for Cell Biology (ASCB) is a diverse conference covering all topics in cell biology. While all of the basic biology presented at this meeting may potentially contribute to breast cancer research, there were a significant number of presentations and posters directly pertinent to this field. Here we have summarized the research that is of greatest immediate relevance to breast cancer, with particular emphasis on mammary gland development and tumorigenesis in vivo, three-dimensional in vitro models of mammary morphogenesis, alterations of signal transduction pathways in breast cancer, and global studies in expression profiling and drug screening.

Abstract 2472: β1 integrin-mediated repair of double-strand breaks in the mouse mammary gland

Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL β 1 integrin signaling has been implicated in the progression and metastasis of various cancers and has been shown to facilitate resistance to radiation therapy. Our laboratory showed that extracellular matrix (ECM) signaling via β1 integrin downregulates homologous recombination (HR), as well as ionizing radiation (IR) induced foci formation of γ-H2AX, RAD51, and MRE11 in single non-dividing cells of a non-tumorigenic human breast epithelial cell line. When the cells were allowed to form junctions, ECM had the opposite effect on repair. Mouse mammary epithelial cells in primary culture behaved as junctioned human breast epithelial cells, upregulating HR and IR induced γ-H2AX foci formation. These results suggested the importance of the tissue microenvironment including cell-cell junctions. Here we hypothesized that β1 integrin-mediated repair depends on the context including homotypic and heterotypic cellular interactions. To test this hypothesis, we studied the effect of β1 integrin in the mouse mammary gland in vivo on DNA repair relevant outcomes. For determining the β1 integrin effect on foci kinetics, mice were intraperitonially injected with the function-blocking antibody Ha2/5 or control IgG. 24 hrs later, the mice were subjected to 6 Gy IR and the level of γ-H2AX foci formation determined by counting Z-stacks of confocal microscopy images. We found that blocking the β1 integrin receptor significantly decreased γ-H2AX foci formation at 15 min, 1 hr, and 2 hrs post IR. These time points correlated with both the formation and disappearance kinetics of the foci. Both the β1 blocked and control mammary glands resolved all foci successfully by 4 hrs, suggesting that overall repair was not attenuated by systemic β1 integrin blocking. We have also ablated the ITGB1 gene using the Cre/loxP recombination system. Cre endonuclease was delivered by up-the-teat injections into 8-12 week old pre-pubertal mice, epithelial organoids were isolated, β1 integrin and Cre endonuclease expression are determined by immunocytochemistry. Cre recombinase was successfully delivered to the ductal epithelial cells by up-the-teat viral injection, and resulted in reduced β1 integrin expression in ∼80% of the organoids isolated from injected mice. In addition MMTV/Cre and ITGB1 floxed mice were crossed to successfully excise the β1 integrin gene and reduce protein expression in the mammary glands of mice aged 10-13 weeks. Experiments are in progress to determine the effects of local and complete β1 integrin gene ablation on IR induced repair foci kinetics. These observations provide the proof-of-principle that ECM has a normal function in maintaining DNA repair processes via β1 integrin signaling in the complex in vivo microenvironment of the mouse mammary gland as well as in cultured cells. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2472. doi:10.1158/1538-7445.AM2011-2472