Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene.

We show here that quantitative measurement of DNA copy number across amplified regions using array comparative genomic hybridization (CGH) may facilitate oncogene identification by providing precise information on the locations of both amplicon boundaries and amplification maxima. Using this analytical capability, we resolved two regions of amplification within an approximately 2-Mb region of recurrent aberration at 20q13.2 in breast cancer. The putative oncogene ZNF217 (ref. 5) mapped to one peak, and CYP24 (encoding vitamin D 24 hydroxylase), whose overexpression is likely to lead to abrogation of growth control mediated by vitamin D, mapped to the other.

High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays.

Gene dosage variations occur in many diseases. In cancer, deletions and copy number increases contribute to alterations in the expression of tumour-suppressor genes and oncogenes, respectively. Developmental abnormalities, such as Down, Prader Willi, Angelman and Cri du Chat syndromes, result from gain or loss of one copy of a chromosome or chromosomal region. Thus, detection and mapping of copy number abnormalities provide an approach for associating aberrations with disease phenotype and for localizing critical genes. Comparative genomic hybridization (CGH) was developed for genome-wide analysis of DNA sequence copy number in a single experiment. In CGH, differentially labelled total genomic DNA from a 'test' and a 'reference' cell population are cohybridized to normal metaphase chromosomes, using blocking DNA to suppress signals from repetitive sequences. The resulting ratio of the fluorescence intensities at a location on the 'cytogenetic map', provided by the chromosomes, is approximately proportional to the ratio of the copy numbers of the corresponding DNA sequences in the test and reference genomes. CGH has been broadly applied to human and mouse malignancies. The use of metaphase chromosomes, however, limits detection of events involving small regions (of less than 20 Mb) of the genome, resolution of closely spaced aberrations and linking ratio changes to genomic/genetic markers. Therefore, more laborious locus-by-locus techniques have been required for higher resolution studies. Hybridization to an array of mapped sequences instead of metaphase chromosomes could overcome the limitations of conventional CGH (ref. 6) if adequate performance could be achieved. Copy number would be related to the test/reference fluorescence ratio on the array targets, and genomic resolution could be determined by the map distance between the targets, or by the length of the cloned DNA segments. We describe here our implementation of array CGH. We demonstrate its ability to measure copy number with high precision in the human genome, and to analyse clinical specimens by obtaining new information on chromosome 20 aberrations in breast cancer.

Oxidative stress pathways highlighted in tumor cell immortalization: association with breast cancer outcome.

An improved understanding of cell immortalization and its manifestation in clinical tumors could facilitate novel therapeutic approaches. However, only rare tumor cells, which maintain telomerase expression in vitro, immortalize spontaneously. By expression-profiling analyses of limited-life primary breast tumor cultures pre- and post-hTERT transduction, and spontaneously immortalized breast cancer cell lines, we identified a common signature characteristic of tumor cell immortalization. A predominant feature of this immortalization signature (ImmSig) was the significant overexpression of oxidoreductase genes. In contrast to epithelial cells derived from low histologic grade primary tumors, which required hTERT transduction for the acquisition of ImmSig, spontaneously immortalizing high-grade tumor cultures displayed similar molecular changes independent of exogenous hTERT. Silencing the hTERT gene reversed ImmSig expression, increased cellular reactive oxygen species levels, altered mitochondrial membrane potential and induced apoptotic and proliferation changes in immortalized cells. In clinical breast cancer samples, cell-proliferation-pathway genes were significantly associated with ImmSig. In these cases, ImmSig expression itself was inversely correlated with patient survival (P=0), and was particularly relevant to the outcome of estrogen receptor-positive tumors. Our data support the notion that ImmSig assists in surmounting normal barriers related to oxidative and replicative stress response. Targeting a subset of aggressive breast cancers by reversing ImmSig components could be a practical therapeutic strategy.

Internal antigens accessible in breast cancer: implications for tumor targeting.

Proponents of monoclonal antibody (MAb)-mediated cancer therapy often assume that a major limitation in clinical application of MAbs is their lack of absolute specificity for malignant cells. In addition, the presence of surface target antigens is thought to be essential. These requirements may be more stringent than necessary for the clinical usefulness of MAbs. We have demonstrated selective localization of a MAb to keratin polypeptides in malignant breast epithelium under conditions of passive infusion of antibody in fresh surgical specimens of breast carcinoma. Although these proteins are normal intracellular constituents of epithelial cells throughout the body, localization of antikeratin antibodies only within the tumor population is most probably associated with the presence of cells permeable to macromolecules. This permeable tumor cell fraction could be recruited for targeting neighboring impermeable tumor cells with radioisotopes or other antitumor agents conjugated to antibodies directed against intracellular antigens.

Expression of basal and luminal epithelium-specific keratins in normal, benign, and malignant breast tissue.

We characterized the subclass-specific keratins in the epithelium of normal, benign, and malignant breast tissue. Monoclonal antibody 34BE12 stained luminal as well as basal epithelium in normal and benign specimens and all tumor cells in malignant specimens. Antibody 312CS-1 reacted only with basal cells, and antibody LE61 reacted only with luminal cells in the normal and benign specimens. In 34 of 36 breast carcinomas examined, the basal and luminal cell-specific antibodies showed complementary patterns of reactivity, while in the remaining 2 specimens, neither antibody was reactive. The findings reported in this study demonstrate that expression of subclass-specific keratins is mutually exclusive not only in normal and benign mammary specimens but also in breast carcinoma. These findings suggest a role for epithelial subclass-specific antibodies in the histogenetic and prognostic subclassifications of breast carcinoma.

Immortalization in culture: occurrence at a late stage in the progression of breast cancer.

The properties in culture of 3 breast cancer effusion metastases, obtained over approximately 2 years from the same patient, were examined. Despite repeated attempts with cryopreserved cells, only the last specimen reproducibly exhibited immortality in culture; the first 2 specimens grew initially but failed to develop into cell lines. Each specimen was unique in morphology and growth properties, although karyotypic markers indicated a common origin. Aberrations of chromosomes 1 and 11 marked these near-diploid cells, and further structural alterations of chromosome 11 accompanied the transition of biological properties observed in the third specimen.

Selective cell culture of primary breast carcinoma.

We have used culture conditions which simulate the microenvironment of breast tumors for the isolation and propagation of primary breast tumor cells in vitro. In this monolayer setup, the mixture of cells dissociated from primary breast tumors is subjected to self-created gradients of oxygen and nutrients as well as metabolic waste and extracellular pH. The tumor populations isolated under these novel conditions have displayed phenotypic properties characteristic of breast carcinomas, including homogeneous expression of cytokeratin 19, and increased mitochondrial retention of the cationic dye rhodamine 123. Nonmalignant cultures from reduction mammoplasty were unable to survive these conditions. One tumor population which reached passage 10 was aneuploid for chromosomes 15 and 17, and displayed a p53 mutation in exon 8. These studies strongly suggest that the culture conditions described here can suppress the growth of normal breast cells, thereby allowing selective isolation of some populations of slow-growing primary tumor cells in vitro.

Partial enzymatic degradation of stroma allows enrichment and expansion of primary breast tumor cells.

The goal of this study was to isolate and expand tumor cells in culture that closely resemble invasive cells in primary breast carcinoma tissue. Based on the hypothesis that invasive tumor cells are released more readily upon digestion with connective tissue-degrading enzymes because they are not confined within a basement membrane, we have designed a novel procedure for their isolation. Using this method, we have successfully expanded in culture aneusomic tumor cells from several primary breast tumors. Twenty nine of 44 (66%) specimens processed yielded proliferative and passageable cultures of up to 2 x 10(7) cells. The original tumor tissue and cultures derived therefrom were compared for aneusomy and the abnormal expression of the erb-B2, p53, and bcl-2 gene products. Remarkable similarities were observed. However, some intratumor heterogeneity in chromosome content was found between touch preparations and cultured cells. Overexpression of erb-B2 was observed in the vast majority of cases (16 of 20), suggesting that this phenotype may be important for dysregulated proliferation in vitro. The simple and rapid method described in this report could enable routine expansion of primary breast tumors and provide adequate numbers of viable cells for studying and manipulating their functional characteristics.

Propagation of genetically altered tumor cells derived from fine-needle aspirates of primary breast carcinoma.

Because primary breast tumors are diagnosed earlier in the clinic, procurement of sufficient amounts of tumor tissue for in-depth biological characterization is becoming increasingly difficult. We demonstrate here that relatively small numbers of tumor cells within samples of fine-needle aspirates (FNA) can be propagated in culture. Of 25 cases attempted, 12 were passageable, resulting in up to 10(7) viable cells. FNA-derived cultures were evaluated for anchorage-independence, c-erb-B2 overexpression, aneusomy, and pattern of allelic loss. In every case examined, the cultured cells closely resembled the original tumor tissue and displayed one or more tumor phenotypes. The incidence of erb-B2 overexpressing tumors was similar in passageable and nonpassageable cases (33% versus 31%, respectively). FNAs that are expanded from a wide range of clinical breast material could be useful for functional studies presently limited to rare established cell lines, such as aberrant signal transduction and gene regulation, and for testing potential anticancer vaccines and drugs.

The human homologue for the Caenorhabditis elegans cul-4 gene is amplified and overexpressed in primary breast cancers.

Amplification is a key mechanism whereby a cancer cell increases the message level of genes that confer a selective advantage when they are overexpressed. In breast cancer, there are many chromosome regions present in multiple copies relative to overall DNA copy number (amplicons), and their target genes are unknown. Using differential display, we have cloned and sequenced the full coding region of a candidate amplicon target gene located on chromosome 13. This candidate is the human homologue of the Caenorhabditis elegans cul-4 gene, cul-4A, a member of the novel cullin gene family, which is involved in cell cycle control of C. elegans. cul-4A was amplified and overexpressed in 3 of 14 breast cancer cell lines analyzed, and it was overexpressed in 8 additional cell lines in which it was not amplified. The latter observation, indicating that its overexpression can occur by mechanisms other than gene amplification, suggests that cul-4A plays a key role in carcinogenesis. Moreover, cul-4A was found to be amplified in 17 of 105 (16%) cases of untreated primary breast cancers, and 14 of 30 cases analyzed (47%) were shown by RNA in situ hybridization to overexpress cul-4A. These results suggest that up-regulation of cul-4A may play an important role in tumor progression.

Characterization of epimyoepithelial islands in benign lymphoepithelial lesions of major salivary gland: an immunohistochemical and ultrastructural study.

Knowledge of the processes leading to the development of epimyoepithelial islands bears on histogenetic and morphogentic processes in salivary gland tumors. Immunohistochemical and ultrastructural investigations of the cellular composition of epimyoepithelial islands were carried out on three examples of benign lymphoepithelial lesions with varying histologic features. The monoclonal anti-keratin antibody 312C8-1, which specifically decorates myoepithelial cells of the normal salivary gland, also stains the myoepithelial cells surrounding residual acini and intercalated ducts in benign lymphoepithelial lesions and the cell population of epimyoepithelial islands, with the exception of persisting luminal epithelial cells. Ultrastructurally, the myoepithelial cells of involuting acini and ducts and the modified myoepithelial cells of epimyoepithelial islands, identified in both locations by the monoclonal antibody 312C8-1, show an increasing complement of tonofilament bundles. In addition, persisting lumens (often distended with lymphocytes) and definite luminal epithelial cells can be seen in electron micrographs of some epimyoepithelial islands. The designation for this characteristic epithelial feature of benign lymphoepithelial lesions is therefore appropriate.

Negative regulation of UCP2 by TGFß signaling characterizes low and intermediate-grade primary breast cancer.

The histological manifestation of growth-regulating and differentiation-inducing signals in cancer cells is considered as a key component for clinical outcome prediction and commonly defined as tumor differentiation grade. However, the molecular and functional framework underlying this clinical parameter remains poorly understood. Our correlative data display a significant association (P>0.001) between mitochondrial uncoupling protein 2 (UCP2) and tumor grade in primary breast cancer (n=234). Through mechanistic analyses, we show a synergistic link between UCP2 and established cellular pathways in conferring grade-associated functional phenotypes. Here, the application of well to moderately differentiated primary tumor cell lines has enabled direct observation of SMAD recruitment to the UCP2 promoter underlying repression of gene transcription. In contrast, poorly differentiated tumor cells, known to be TGFß resistant, displayed aberrant UCP2 regulation, and consequently, gene overexpression, which reduced mitochondrial calcium and facilitated the maintenance of mitochondrial membrane potential, thereby significantly decreasing oxidative stress and inhibiting cell death. Conversely, UCP2 silencing in such cells rapidly led to the induction of apoptosis and cell differentiation, concurrent with reduced cell survival and proliferation, confirming gene-specific effects. Demonstration of a biologically driven role for UCP2 dysregulation in promoting multiple characteristics of tumor aggressiveness strongly endorses assessment of gene expression at clinical presentation to augment therapeutic decision-making and improve patient outcome through personalized targeting approaches.

Differential retention of rhodamine 123 by breast carcinoma and normal human mammary tissue.

We have qualitatively evaluated the retention of the fluorescent dye rhodamine 123 by malignant or non-malignant breast epithelial cells in passively-infused fresh surgical specimens. Our findings demonstrate a microscopically-visible increase in the ability of primary and metastatic tumor cells to retain the dye, as compared to non-malignant epithelium. Some variability in fluorescence intensity was seen within and between tumor specimens. The optimal length of incubation in the presence of the dye was critical in achieving differential fluorescence intensity between normal and malignant cells. This method of examining rhodamine 123 uptake and retention in tissue explants provides a reliable means for direct, comparative visualization in situ of any tissue and its associated disorders. The results of this study also demonstrate the validity of extending the use of lipophilic, cationic compounds such as rhodamine 123 as antitumor agents, from model systems to the treatment of malignant disease.

Genetic analysis of breast cancer progression.

At the histological level, breast tumors display a variety of morphologic lesions which suggest the existence of an increasingly aberrant pathway of intermediate steps leading to the invasive primary tumor and its metastatic dissemination. In order to obtain direct evidence for this presumed progression, underlying genetic changes must be identified. Analyses of primary breast tumors have revealed a large number of dominant and recessive gene alterations encompassing several cellular attributes and activities. It is quite likely that some of these alterations are of a causal nature and thus enable the tumor to attain distinctive malignant phenotypes, such as, dysregulated proliferation, invasion, angiogenesis, and ability to metastasize. Considerable heterogeneity has been observed in the sequence of acquisition of these genetic changes, which is substantiated by recent comparative analyses between carefully microdissected preinvasive and invasive tumor. The data are evaluated here in the context of existing models of breast cancer progression. Implication and prospects for translational application to the clinic are also discussed.

Dimethyl sulfoxide affects colony morphology on agar and alters distribution of glycosaminoglycans and fibronectin.

We have found striking changes in the morphology of colonies of Chinese hamster ovary cells grown on agar containing low doses of dimethyl sulfoxide. Effects on morphology of cells grown on plastic at the same dimethyl sulfoxide concentrations were not as pronounced. Computer-assisted analysis of darkfield photographs of growing colonies proved very useful in measuring the magnitude of morphological changes at various doses. A large decrease in total cell-bound and released glycosaminoglycans (GAGs) was observed in the presence of dimethyl sulfoxide by measuring incorporation of radiolabeled precursors into cetylpyridinium chloride-precipitable GAGs in Chinese hamster ovary cells. By contrast, dimethyl sulfoxide was found to cause an increase in the network of fibronectin (the large external transformation-sensitive protein) at the cell surface. These observations demonstrate the association of GAGs and fibronectin in processes affecting the three-dimensional growth patterns of aggregates of mammalian cells and also demonstrate the sensitivity of agargrown colonies as model systems for quantitatively measuring the morphological changes induced by exogenous agents such as drugs, hormones, growth factors, mutagens, and carcinogens. These findings might be relevant to the study and treatment of the important class of genetic diseases called mucopolysaccharidoses which result in mental, skeletal, and ocular defects as a consequence of GAG accumulation.

Production of factors required for cell attachment and spreading is a constitutive property in mouse A9 cells.

It is demonstrated here that cells in a suspension culture of an established mammalian cell line release non-dialyzable factors into their growth medium. These factors are capable of promoting the adhesion and spreading of these cells on a generally non-attachable substratum and also promote spreading on an adhering substrate. Evidence is presented which demonstrates that the spreading promotion activity of the condition medium is dependent on the cell density of the culture from which it was derived. Dilution of the conditioned medium results in a proportionate dilution of the spreading promotion activity. The results clearly demonstrate that the production of this spreading promotion factor is continued even in the absence of cell to substrate attachment.

A mutagen-testing assay based on heterogeneity in diameter and integrated optical density of mammalian cell colonies.

We investigated the effects of the well-known mutagenic agents ethyl methanesulfonate (EtMes), N-methyl-N-nitro-N-nitrosoguanidine (MNNG), and ICR-191 on colonies of the Chinese hamster ovary line CHO cultured on a semisolid substrate. These agents induced heterogeneity in diameter and integrated optical density of colonies as determined by computer-assisted photography and subsequent analysis of the images of the colonies. When CHO colonies were exposed to agents such as urethane that are not known to be mutagenic in mammalian systems or to activation-requiring mutagens such as cyclophosphamide, there was no noticeable effect on the distribution of colony diameter and volume. Similarly, nonmutagenic agents such as dimethyl sulfoxide (Me2SO) also did not induce heterogeneity in colony diameter and integrated optical density. Our observations recommend the use of agar-grown mammalian cell colonies for predictive testing of chemical mutagens and carcinogens in a simple, in vitro mammalian cell assay. This assay system, unlike other mammalian cell culture assays, allows detection and measurement of the simultaneous effects of chemical mutagens on several genetic and non-genetic targets and, thus, may emulate more closely the potential hazards of these agents in vivo.

Colony morphology on agar is a sensitive indicator for growth effectors.

Colonies of Chinese hamster ovary (CHO) cells growing on agar exhibit changes in colony morphology and size in response to extremely low doses of hormones and growth factors. Computer-aided densitometric scanning of photographs of these colonies allows the quantitative measurement of these morphological changes. Correlation of these changes with dosage for a variety of growth effectors is a sensitive assay for the effects of these factors, both alone and in combination, and should be useful in comparing effects of agents with similar biological activities and in the search for variant cell types with altered responsiveness. Cells growing attached to solid substrates are often responsive to these low dosages and do not seem to mimic in vivo growth effector phenomena as well as colonies growing in three dimensions on agar.

Response of primary human mammary tumor cell cultures to a monoclonal antibody-recombinant ricin A chain immunotoxin.

Malignant epithelial tumor cells were isolated and cultured from ten human mammary specimens of cancerous origin. The 260F9 monoclonal antibody (MAB) bound to frozen sections of all of the human breast tumors tested and to primary cultured cells from the tumors. Cultured cells from all ten breast tumors were sensitive to the clonal inhibitory effects of immunotoxin 260F9 MAB-recombinant ricin A chain. At an immunotoxin concentration of 200 ng/ml (about 1 nM), inhibition of colony formation was greater than 99% for all ten tumors.

Immunolocalization of a human basal epithelium specific keratin in benign and malignant breast disease.

This report describes the immunocytochemical localization of a human basal- or myoepithelial-specific anti-keratin antibody in benign and malignant breast disease. Reactivity patterns with this antibody have demonstrated the lack of myoepithelial or basal epithelial participation in most benign breast specimens examined including those displaying cystic disease, fibrosis, or hyperplasia. However, in specimens of sclerosing adenosis, strong reactivity with the majority of cells in most ducts suggests a major participation of the myoepithelial cell type. Analysis of 118 breast carcinoma specimens has demonstrated strong, homogeneous reactivity in 4% of the specimens, suggesting a role for the basal epithelial cell in malignancy of the human mammary gland and implications for the prognosis of such tumors. Antigenic characterization of the malignant and benign mammary specimens which are uniformly reactive with the antibody has demonstrated the presence of a 51 kd keratin polypeptide not found in the non-reactive specimens.