Identification of gene expression profiles that predict the aggressive behavior of breast cancer cells.

With the goal of identifying genes that have an expression pattern that can facilitate the diagnosis of primary breast cancers (BCs) as well as the discovery of novel drug leads for BC treatment, we used cDNA hybridization arrays to analyze the gene expression profiles (GEPs) of nine weakly invasive and four highly invasive BC cell lines. Differences in gene expression between weakly and highly invasive BC cells were identified that enabled the definition of consensus GEPs for each invasive phenotype. To determine whether the consensus GEPs, comprising 24 genes, could be used to predict the aggressiveness of previously uncharacterized cells, gene expression levels and comparative invasive and migratory characteristics of nine additional human mammary epithelial cell strains/lines were determined. The results demonstrated that the GEP of a cell line is predictive of its invasive and migratory behavior, as manifest by the morphology of its colonies when cultured on a matrix of basement membrane constituents (i.e., Matrigel). We found that the expression of keratin 19 was consistently elevated in the less aggressive BC cell lines and that vimentin and fos-related antigen-1 (FRA-1) were consistently overexpressed in the more highly aggressive BC cells. Moreover, even without these three genes, the GEP of a cell line still accurately predicted the aggressiveness of the BC cell, indicating that the expression pattern of multiple genes may be used as BC prognosticators because single markers often fail to be predictive in clinical specimens.

Identification of AKT-regulated genes in inducible MERAkt cells.

AKT/protein kinase B plays a critical role in the phosphoinositide 3-kinase (PI3-kinase) pathway regulating cell growth, differentiation, and oncogenic transformation. Akt1-regulated genes were identified by cDNA array hybridization analysis using an inducible AKT1 protein, MERAKT. Treatment of MERAkt cells with estrogen receptor ligands resulted in phosphorylative activation of MERAKT. Genes differentially expressed in MERAkt/NIH3T3 cells treated with tamoxifen, raloxifene, ICI-182780, and ZK955, were identified at 3 and 20 h. AKT activation resulted in the repression of c-myc, early growth response 1 (EGR1), transforming growth factor beta receptor III (TGF-betar III), and thrombospondin-1 (THBS1). Although c-myc induction is often associated with oncogenic transformation, the c-myc repression observed here is consistent with the anti-apoptotic function of AKT. Repression of THBS1 and EGR1 is consistent with the known pro-angiogenic functions of AKT. AKT-regulated genes were found to be largely distinct from platelet-derived growth factor-beta (PDGFbeta)-regulated genes; only T-cell death-associated gene 51 (TDAG51) was induced in both cases. In contrast to their repression by AKT, c-myc, THBS1, and EGR1 were induced by PDGFbeta, indicating negative interference between elements upstream and downstream of AKT1 in the PDGFbeta signal transduction pathway.

In situ hybridization for gastrin-releasing peptide receptor (GRP receptor) expression in prostatic carcinoma.

Bombesin-like peptides (BLPs), which have been implicated in the regulation of growth of prostatic carcinoma cells, are a product of neuroendocrine cells frequently found in prostate tissue and are postulated to play a role in the initiation or progression of prostatic carcinoma. In this report, we examined the expression, in human prostate tissue, of mRNA encoding the 3 known receptors that respond to BLPs in humans, i.e., gastrin-releasing peptide (GRP) receptor, neuromedin B (NMB) receptor and bombesin receptor subtype 3 (BRS-3). Competitive rt-PCR experiments demonstrated the widespread but variable expression of GRP receptor mRNA in fresh-frozen specimens of prostatic carcinoma (12 cases) and benign prostatic hypertrophy (6 cases). NMB receptor mRNA expression was also widespread, but its level was less variable than GRP receptor message. In contrast, we could not detect BRS-3 mRNA in most tissue samples by rt-PCR. To address which cells in the prostate express the GRP receptor, we used in situ hybridization methods to stain selectively GRP receptor mRNA. GRP receptor mRNA was expressed predominantly in the luminal and basal epithelial cells in both histologically normal and cancerous glands within sections of normal (3 cases) and diseased (37 cases) tissue. GRP receptor mRNA staining in cancerous tissue ranged widely from very intense to not detectable (about 30% of the cases), while normal tissue consistently displayed a low level of message staining. Taken together, our results demonstrate expression of the GRP receptor in a high percentage of basal and/or luminal epithelial cells of normal and diseased prostate tissues.

Bombesin-like peptide receptor subtypes promote mitogenesis, which requires persistent receptor signaling.

Bombesin-like peptides (BLPs) can regulate the growth of normal and transformed cells. To compare the relative activities of the three known human BLP receptor subtypes [i.e., the gastrin-releasing peptide (GRP) receptor, neuromedin B (NMB) receptor, or BLP receptor subtype 3] in growth regulation, we expressed each receptor in a receptor-deficient host, Balb/3T3 cells. None of the receptor agonists used in our study promoted DNA synthesis by quiescent parental, nontransfected Balb/3T3 cells. Using clones stably transfected with the NMB receptor however, we found that NMB stimulated the incorporation of [3H]thymidine 2.5- to 8-fold over basal levels. The greatest net stimulation of [3H]thymidine incorporation occurred when the medium contained insulin. In quiescent Balb/3T3 cells transfected with the GRP receptor, GRP promoted a 15-fold increase in DNA synthesis in the absence of insulin or other growth factors. GRP also induced the labeling of a large percentage (53%) of the cells with bromodeoxyuridine. To determine the length of time that GRP receptor signaling was required to drive quiescent cells into the S phase of the cell cycle, we blocked GRP receptor signaling by addition of a competitive GRP receptor antagonist at different times after stimulating cells with GRP. Our data demonstrate that persistent GRP receptor signaling throughout a large part of the G1 phase of the cell cycle is important in the mitogenic effects of GRP in these cells. Hitherto uncharacterized GRP receptor signaling pathways may be important in this process. BLPs also stimulated a mitogenic response by transfectants expressing the BLP receptor subtype 3 if insulin was contained in the medium. Taken together, these studies indicate that all three BLP receptor subtypes may contribute to growth regulation in vivo.

Nuclear distribution of centromeres during the cell cycle of human diploid fibroblasts.

The distribution of centromeres in the interphase nuclei of human diploid fibroblasts was analyzed using anti-centromere immunofluorescence and laser scanning confocal microscopoy. The positions of the centromeres were placed within the nuclear chromatin distribution and presented some aspects of the dynamics of nuclear structure during the cell cycle. During the G1 phase of the cell cycle many of the centromeres were located in association with nucleoli or fused in chromocenters. A few centromeres were dispersed singly in the euchromatin. During S phase, the fused centromeres dispersed, often forming distinct patterns of rings or lines. At prophase, the centromere immunofluorescence condensed into distinct double dots upon the formation of the prophase chromosomes. Quantitative analysis by both image and flow cytometry showed that the intensity of immunofluorescence started to duplicate in mid S phase, well before the appearance of the double dots. The coalesence of the centromeres during G1 indicated that regions of the chromosome domains remain compacted and possibly sequestered from transcriptional activity. During S phase the chromatin and the coalesced centromeres dispersed for DNA replication. The dynamics of the centromeres and chromatin during the cell cycle seen here are evidence for a higher-order organization of nuclear structure that accompanies DNA transcription and replication.

Karyotype evolution in a simian virus 40-transformed tumorigenic human cell line.

Normal human foreskin fibroblasts (HSF4) were transfected using the pSV3-neo plasmid. A pool of 10 G418-resistant colonies, HSF4-T12, showed a progressive increase in the expression of a number of in vitro transformation markers with passage in culture and became immortalized. Although no tumors were formed when cells were injected subcutaneously into nude mice, this cell line produced progressive tumors when cells were injected into preimplanted Gelfoam sponges in the mice. When these tumors were cultured in vitro and subsequently injected subcutaneously, progressive tumors were produced with median latency periods as short as 4 weeks. Three phases of cytogenetic change could be distinguished. At early passages after transfection. HSF4-T12 exhibited many random chromosomal changes. At a time just after immortalization, both flow karyotype and G-banded analyses showed the appearance of balanced clonal rearrangements. These included t(2;4), t(2;14), t(3;?), 6p-, i(6p), 8p-, t(14;15), i(15), and t(18;?). These clonal rearrangements were stable with passage in culture, and less variability from cell to cell was noted. The only consistent chromosomal loss observed was -Y. Analysis of three independent tumors showed characteristic loss of chromosomal material rather than balanced chromosomal rearrangements. Frequent loss of 6q and chromosomes #13, 15, 20, and Y was noted.

System for flow sorting chromosomes on the basis of pulse shape.

Sorting on the basis of the complex features resolved by chromosome slit-scan analysis requires rapid and flexible pulse shape acquisition and processing for determining sort decisions before droplet breakoff. Fluorescence scans of chromosome morphology contain centromeric index and banding information suitable for chromosome classification, but these scans are often characterized by variability in length and height and require sophisticated data processing procedures for identification. Setting sort criteria on such complex morphological data requires digitization and subsequent computation by an algorithm tolerant of variations in overall pulse shape. We demonstrate here the capability to sort individual chromosomes based on their morphological features measured by slit-scan flow cytometry. To do this we have constructed a sort controller capable of acquiring an 128 byte chromosome waveform and executing a series of numerical computations resulting in an area-based centromeric index sort decision in less than 2 ms. The system is configured in a NOVIX microprocessor, programmed in FORTH, and interfaced to a slit-scan flow cytometer data acquisition system. An advantage of this configuration is direct control over the machine state during program execution for minimal processing time. Examples of flow sorted chromosomes are shown with their corresponding fluorescence pulse shapes.

Flow cytogenetics.

Applications of flow karyotype analysis and flow chromosome sorting are being developed and are becoming increasingly relevant to clinical research. Among these applications are the quantitative analysis of chromosomal DNA content changes enabling the detection of minute deletions or unbalanced translocations, the quantitative analysis of aneuploidy for trisomy screening, and the sorting of derivative chromosomes for mapping chromosome breakpoints. Flow karyotyping has been accomplished on samples with clinical relevance including peripheral blood from both children and cancer patients as well as amniotic cell cultures. New techniques in flow cytogenetics to resolve chromosomes by morphology or by DNA sequence hybridizations are assessed for their promise. Although flow karyotyping has not yet developed into an 'automated' karyotyping technique, when used in conjunction with classical cytogenetic techniques, new information of significance to the clinician can be produced.

The t(11;14)(p15;q11) in a T-cell acute lymphoblastic leukemia cell line activates multiple transcripts, including Ttg-1, a gene encoding a potential zinc finger protein.

Interchromosomal translocations within lymphoid neoplasms frequently involve the antigen receptor genes. We cloned the breakpoints of the t(11;14)(p15;q11) in a CD3-negative T-cell acute lymphoblastic leukemia cell line (RPMI 8402) in order to identify new genes potentially involved in T-cell neoplasia. An extensive comparison of both breakpoints and their germ line counterparts indicated that an inadvertant recombinase-mediated break at chromosome segment 11p15 recombined with the delta T-cell receptor at 14q11. The derivative 11 breakpoint resembles a coding joint in which 11p15 rather than a variable region was introduced 5' to a D delta 1 D delta 2 J delta 1 intermediate rearrangement. Conversely, the derivative 14 breakpoint corresponds to a signal joint between the 5' heptamer-spacer-nonamer recombinational signal of D delta 1 and an isolated heptamer at 11p15. Multiple, apparently distinct transcripts were found flanking both breakpoints of 8402. RNAs of 3.5, 4.4, 1.4, and 8.0 kilobases originating from either side of the derivative 14 breakpoint were highly expressed in 8402 compared with other cells. This suggests that this translocation deregulated multiple genes and provides the opportunity to assess any multifactorial contribution they may have to malignancy. We cloned and sequenced several cDNAs representing the 1.4-kilobase transcript (termed Ttg-1 [T-cell translocation gene 1]) from an 8402 library. The predicted protein of 156 amino acids contained two internal repeats which could potentially form zinc fingers.

Chromosome banding analysis by slit-scan flow cytometry.

We have investigated the use of fluorescence banding patterns for the resolution of metaphase chromosomes by slit-scan flow cytometry. Fluorescence scans of R-banded chromosomes have been obtained for the entire human karyotype. Metaphase chromosomes were R-banded in suspension by staining with chromomycin A3 after hypotonic treatment in Ohnuki's buffer. Specific fluorescent landmark bands were detected for human chromosomes 1-12. Scans obtained for chromosomes 13-22 did not contain sufficient information for classification. Characteristic fluorescence patterns for human chromosomes 1 and 3 provided the clearest evidence for the detection of R-bands by slit-scan flow cytometry. Specific patterns were detected for human chromosomes 9-12 in which the number and placement of the fluorescent bands served as classifiers.

The clinical usefulness of chromosome analysis by flow cytometry.

Historical and clinical aspects of chromosome analysis by flow cytometric methods are reviewed. A new method of preparing small samples (1.0 mL of blood) of peripheral lymphocytes for flow karyotype analysis using phytohemagglutinin and interleukin-2 is presented in detail. Figures of flow karyotypes, partial banded karyotypes, and idiograms of patients with inv(8), rec dup(8), rob t(14;21), and t(1;22) are presented, as well as examples of univariate and bivariate flow histograms from other researchers' published works. The clinical utility of these techniques is explored, with specific reference to recent work in chromosome polymorphisms and cultured amniocyte lines. We conclude that, although flow karyotyping is not a replacement for classical banded chromosome analysis, used as an adjunct, this new technique has some clinical usefulness relating to its capability to resolve small differences in chromosomal DNA content.

Spontaneous in vitro neoplastic evolution: selection of specific karyotypes in Chinese hamster cells.

Recurrent cytogenetic changes occurred reproducibly in vitro during the spontaneous neoplastic evolution of cultured Chinese hamster cells. In particular, excess 3q material appeared shortly after immortalization in numerous independent trials. By contrast, when clones were isolated at the earliest possible time after immortalization, a wide spectrum of types of cytogenetic evolution followed, which also resulted in transformed and tumorigenic cells. Clones with stable distinct colonial morphologies were used to demonstrate growth rate interactions when subpopulations compete. We conclude that specific recurring karyotypes are associated with specific stem lines with transient growth advantage during the early stages of in vitro carcinogenesis. Stem lines with other karyotypic change or no detectable karyotypic change are almost equally capable of undergoing the entire spontaneous neoplastic process in vitro.

Human chromosome-specific repetitive DNA sequences: novel markers for genetic analysis.

Two recombinant DNA clones that are localized to single human chromosomes were isolated from a human repetitive DNA library. Clone pHuR 98, a variant satellite 3 sequence, specifically hybridizes to chromosome position 9qh. Clone pHuR 195, a variant satellite 2 sequence, specifically hybridizes to chromosome position 16qh. These locations were determined by fluorescent in situ hybridization to metaphase chromosomes, and confirmed by DNA hybridizations to human chromosomes sorted by flow cytometry. Pulsed field gel electrophoresis analysis indicated that both sequences exist in the genome as large DNA blocks. In situ hybridization to intact interphase nuclei showed a well-defined, localized organization for both DNA sequences. The ability to tag specific human autosomal chromosomes, both at metaphase and in interphase nuclei, allows novel molecular cytogenetic analyses in numerous basic research and clinical studies.

Karyotype instability of Chinese hamster cells during in vivo tumor progression.

The extent of karyotype instability in spontaneously transformed Chinese hamster cells was determined after tumor formation by cytogenetic analysis of karyotype heterogeneity. The degree of karyotype heterogeneity among tumors formed in nude mice correlated with tumor latent period. The karyotypes of tumors formed after a short latent period by cells of high tumorigenic potential were similar to each other and to the injected cells. The karyotypes of tumors from cells of low tumorigenic potential and long latents periods were diverse, however. No chromosome aberration was common to every tumor. These results suggest that preneoplastic cells whose phenotypes are not directly capable of tumor formation can progress in vivo and that karyotype instability plays an important role in providing cell variants for tumor progression.

Spontaneous immortalization rate of cultured Chinese hamster cells.

Chinese hamster cell cultures derived from either fetal cell suspensions or adult ear clippings invariably became permanent cell lines during conventional subcultivation. The immortal cell cultures arose from rare spontaneous cellular events during the in vitro cultivation of cells with limited proliferative capacity. Immortality was not related to rare, precommitted cells from the animals. The expansion of clones of cells with limited life-span to form permanent cell lines was routinely successful only when the initial, unsubdivided culture achieved a total number in excess of 10(6) cells. On the basis of this observation, a serial clonogenicity assay was developed for determining the life-span of the cells with limited proliferative capacity and for determining whether a cell population is immortal. In addition, the technique of clonal expansion was used for a fluctuation analysis to determine the rate of immortalization. This analysis yielded a rate of 1.9 X 10(6) per cell per generation.

Spontaneous in vitro neoplastic evolution: recurrent chromosome changes of newly immortalized Chinese hamster cells.

Spontaneous neoplastic progression in cultured Chinese hamster cells was studied at the earliest stage possible. Eighteen independent newly immortalized cell populations (from six individual Chinese hamsters) were characterized for karyotype instability. Colonies were selected from initial sparse platings of adult or fetal cells and were expanded for study. The chromosomes from these newly established cell lines were studied using a combination of G-banding and flow karyotype analysis. At a slightly later passage, the 18 cell lines were tested for tumorigenicity in nude mice. Frequent recurring chromosome changes were observed in the karyotypes. The most frequent changes were either total or partial trisomy of chromosome #3 (83%) and trisomy of chromosome #5 (61%). Only 4 of 18 clones (22%) were tumorigenic at the time of testing, and these had long latent periods. The presence of recurrent chromosome changes did not obligate these cell lines to become tumorigenic, but the karyotype instability appeared to be an indicator of the ongoing process of neoplasia.

Preneoplastic phenotype and chromosome changes of cultured human Bloom syndrome fibroblasts (strain GM 1492).

The Bloom syndrome fibroblast strain, GM 1492, was examined for phenotypic properties generally associated with neoplastic cells. A serial clonogenicity assay indicated that these cells can proliferate in culture, achieving approximately twice the number of population doublings as compared to normal human skin fibroblasts. Strain GM 1492 appeared to be partially transformed in that these cells showed a slight degree of anchorage independence when grown in methylcellulose, and also appeared to have relaxed growth requirements compared to normal fibroblasts. GM 1492 cells are heteroploid, with 20 to 80 chromosomes/cell and a modal chromosome number of 44. Cytogenetic analysis of G-banded metaphase chromosomes indicated that most cells contained at least one copy of each normal human chromosome, and many cells exhibited only aneuploidies with no detectable chromosomal rearrangements. Minute chromosomes were seen in a few of the metaphase cells examined. GM 1492 cells did not form tumors in athymic nude mice. Since many of the characteristics of GM 1492 cells are similar to those seen only in tumor cells, but the strain is nontumorigenic, we suggest that GM 1492 cells are preneoplastic and thus represent an ideal system for the in vitro study of human neoplastic progression.