Selection of down-regulated sequences along the monocytic differentiation of leukemic HL60 cells

Identification of Taxreb107 as a lactogenic hormone responsive gene in mammary epithelial cells

Mammary gland development and differentiation is regulated by a number of growth factors and hormones. Milk protein gene expression represents a hallmark of functional mammary epithelial differentiation and is coordinated by the lactogenic hormone prolactin and glucocorticoids. To date, few 'early-response' genes transcriptionally activated by lactogenic hormones have been described. We have used representational difference analysis (RDA) to search for lactogenic-responsive genes in SCp2 mouse mammary epithelial cells. One of the cDNAs identified encoded the DNA-binding protein Taxreb107, originally identified as a HTLV-I Tax responsive element binding protein. Increased Taxreb107 expression was confirmed following prolactin and dexamethasone-induced differentiation of SCp2 and HC11 mammary epithelial cells. Taxreb107 RNA levels were developmentally regulated in the mouse mammary gland, where levels increased substantially during mid- and late pregnancy and persisted during lactation. Overexpression of an antisense Taxreb107 cDNA construct or antisense oligonucleotide in HC11 mammary epithelial cells attenuated milk protein gene expression following prolactin and dexamethasone treatment. These findings indicate a role for Taxreb107 as a lactogenic hormone-responsive gene during differentiation of the mammary gland.

Methods for the molecular analysis of cancer. An overview

Cancer arises as a result of complex and interacting abnormalities. However, over the past 20-25 yr numerous technological advances in molecular biology have led to a dramatic increase in the identification of the molecular processes involved in the development of cancers. The analysis of these molecular changes can be done on different levels: at the DNA or RNA level, or by assessment of posttranscriptional events. This overview discusses the merits of different methods for the analysis of DNA such as SSCP or DGCE. The exciting methods of RNA expression analysis using oligo or cDNA gene chips are also discussed. The importance of methods to analyze posttranscriptional or the effect that altered telomerase activity or methylation status contributes to the phenotype of the cancer cell is emphasized. These techniques will contribute to a better understanding of cancer initiation and progression and will eventually lead toward the development of new molecular-targeted drug therapies.

Gene expression of TPA induced differentiation in HL-60 cells by DNA microarray analysis

The tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) is a potent inducer of differentiation in human promyelocytic leukemia cells. Recently, TPA has been successfully administered to patients with myelocytic leukemia and has produced therapeutic effects that led to temporary remission. These studies demonstrated the potential efficacy of TPA in cancer chemotherapy. We now seek to understand the biological effects and molecular mechanisms of differentiation in response to TPA treatment in leukemia cells by expression profiling using DNA microarray. Our results show distinct temporal and coordinated gene changes that are consistent with differentiation and activation of multiple biochemical pathways in HL-60 cells exposed to TPA. Alterations of gene expression in HL-60 cells include various transcription factors, cytokines and protein markers that are consistent with the induction of differentiation elicited by TPA. These temporal patterns of gene expression were abolished or greatly diminished in an HL-60 derived TPA- resistant variant cell line (HL-525), thus revealing transcriptional and consequential biochemical changes that may be required for TPA-induced differentiation. In addition, certain genes were upregulated by TPA in TPA-resistant HL-525 cells but not in TPA-sensitive HL-60 cells suggesting that these genes may play a role in the resistant phenotype. These patterns of gene expression may be important for predicting response to TPA.

Subtractive hybridization--genetic takeaways and the search for meaning

Gene expression profiling relies on mRNA extraction from defined cell systems, which in the case of pathological processes necessarily results in the use of small quantities of tissues, sometimes as little as a few cells. This obviates the use of many systems of gene expression profiling and is best carried out using cDNA amplified by poly(A) reverse transcription polymerase chain reaction, which is capable of generating material representative of all the expressed genes in samples as small as one cell. Analysis of this material using subtractive hybridization compares the genes expressed at different stages of a biological/pathological process allowing identification of the all the genes upregulated during the process. The identification of the genes present is not dependent on their prior description or on the choice of genes used in a screen and as such the method is ideal for identifying novel genes or unsuspected genes. We have used the method to identify genes involved in normal osteoblastic differentiation and in Paget's disease of bone and it has been widely used to study normal differentiation and pathological processes in a number of systems. The method, its applications and its relationship with the other methods of gene expression profiling are reviewed.

Expression analysis of human HL60 cells exposed to 60 Hz square- or sine-wave magnetic fields

A total of 960 complementary DNA (cDNA) clones from an HL60 cell cDNA library were screened to discover genes that were differentially expressed in HL60 cells exposed to 60 Hz square-wave magnetic fields (MFs) compared to sham-exposed cells. Square-wave fields are rich in odd harmonic frequency content. We used a two-gel cDNA library screening method (BIGEL) to identify treatment-induced alterations in gene expression. Four cDNA clones were tentatively identified as differentially expressed after exposure to square-wave MFs at 2 mT for 24 h. BIGEL-identified genes (GenBank accession number) corresponding to these clones were: TI227H (D50525), EST Homo sapiens partial cDNA (Z17814), human ribosomal protein S13 (L01124), and AICAR transformylase mRNAs (D82348). The differences in mRNA levels were not confirmed in test compared to experimental cells by Northern analysis. In other experiments, we used concurrent exposure to 60 Hz sine- or square-wave MFs (0 or 2 mT, duration of 3 or 24 h, no postexposure delay). In addition to the four BIGEL genes, we also investigated MYC, HSP70, RAN and SOD1. In the case of MYC and HSP70, square-wave MFs appeared to exhibit more marked alterations when compared to sinusoidal waveforms, but the overall results indicated no effect of possible differential magnetic-field-induced expression of all eight genes. In contrast, alterations of mRNA levels were observed for seven genes after exposure to X irradiation, hyperthermia and TPA. These results are contrary to previously proposed similarities between the action of these agents and MF effects on gene transcription.

Ribosomal proteins in cell proliferation and apoptosis

Ribosomal proteins have the complex task of coordinating protein biosynthesis to maintain cell homeostasis and survival. Recent evidence suggests that a number of ribosomal proteins have secondary functions independent of their involvement in protein biosynthesis. A number of these proteins function as cell proliferation regulators and in some instances as inducers of cell death. Specifically, expression of human ribosomal protein L13a has been shown to induce apoptosis, presumably by arresting cell growth in the G2/M phase of the cell cycle. In addition, inhibition of expression of L13a induces apoptosis in target cells, suggesting that this protein is necessary for cell survival. Similar results have been obtained in the yeast Saccharomyces cerevisiae, where inactivation of the yeast homologues of L13a, rp22 and rp23, by homologous recombination results in severe growth retardation and death. In addition, a closely related ribosomal protein, L7, arrests cells in G1 and also induces apoptosis. Thus, it appears that a group of ribosomal proteins may function as cell cycle checkpoints and compose a new family of cell proliferation regulators.

IL-2-Dependent Expression of Genes Involved in Cytoskeleton Organization, Oncogene Regulation, and Transcriptional Control

IL-2 induces growth, differentiation, and/or apoptosis of lymphoid cells. To study further the molecular basis of IL-2 function, we used a cDNA subtraction approach involving a cell line grown in IL-2 or IL-4. From the corresponding library, 66 nonredundant sequences were characterized; 16 of them encode identified proteins. The kinetics of in vitro expression of 8 selected sequences, the functions of which could be associated with IL-2-induced T cell activation/differentiation, was investigated using an IL-2-dependent T cell line. IL-2 increased the expression of cytoskeleton proteins (α-tubulin), oncogene-regulating proteins (CCCTC-binding factor, Jun inhibitor factor-1), and transcription factors (E2F-4, cyclic AMP-responsive element-binding protein, zhx-1). IL-2 also regulated the expression of genes coding for multifunctional proteins, e.g., β-catenin and nucleolin. These results were verified using Con A-induced T cell blasts stimulated or not by IL-2. The in vivo expression of four of these genes was also analyzed in spleen and lymph node cells of IL-2-deficient and MRL/lpr mice, which both have high numbers of activated cells, but the latter have intact IL-2 expression. The expression of β-catenin, CCCTC-binding factor, Jun inhibitor factor-1, and nucleolin was significantly higher in MRL/lpr animals. A similar analysis of thymocytes from IL-2−/− and IL-2+/− mice demonstrated the same expression patterns of the 4 sequences in these strains. The expression of the IL-2-induced genes described herein is similar to the regulatory pattern of IL-2Rα. Taken together, our data provide additional evidence for the pleiotropic action of IL-2 in the periphery and IL-2 independence of molecular processes involved in thymocyte differentiation.

Identification of TAXREB107 as an erythropoietin early response gene

The protooncogenes c-myc and c-myb are erythropoietin (Epo)-regulated early response genes. They appear to play distinct roles in the growth- and differentiation-inducing signals of the hormone. Using a subtractive hybridization strategy, we have identified the murine homolog of the TAX response element-binding protein TAXREB107 as an Epo early response gene in Rauscher murine erythroleukemia cells. This was confirmed by Northern blot analyses, which showed a fourfold increase in TAXREB107 mRNA after 1 hr of erythropoietin treatment. After 3 hr the transcript had decreased to approximately twofold above control levels. Inhibition of this induction with antisense oligodeoxynucleotides increased Epo-induced hemoglobinization 2.5-fold. The results implicate TAXREB107 in erythropoiesis and support the hypothesis that the TAXREB proteins have functions outside the context of HTLV-I infection.

Expressed genes in interleukin-4 treated B cells identified by cDNA representational difference analysis

Interleukin-4 (IL-4) stimulates B cell growth and differentiation, such as inducing mature B cells to switch to IgG1 and IgE production. To further characterize IL-4 effects on B cells, we used a sensitive PCR-based subtraction approach to isolate genes expressed in IL-4 treated cells. Our approach combined an adaptation of the genomic representational difference analysis (RDA) method to cDNA analysis with a physical separation method (magnetic bead depletion). This cDNA RDA technique allowed us to perform subtraction on the relatively small number of highly, characterized, purified B cells that can be conveniently prepared. In the hopes of removing genes responsible for general cell growth, we subtracted cDNA made from lipopolysaccharide (LPS)-stimulated B cells from cDNA from LPS+IL-4 stimulated B cells. Two rounds of subtraction resulted in greater than 100-fold enhancement of expected IL-4-induced Cgamma1 cDNA. At that point, we cloned this subtraction library and analysed 154 randomly picked clones for sequence similarities. From these clones, 37 individual genes were obtained. Most of these genes (30) could be functionally identified by sequence similarity. These included genes encoding Cgamma1 (1), cytoskeletal components (4) and products involved in DNA replication (3), metabolism (5), signal transduction (4), transcription (4), translation (6) and transport (3). Only 7 genes had no similarity to known sequences in the GenBank, EMBL or Swiss Prot databases. One unknown gene (designated Fig1 for IL-Four Induced Gene 1) and one gene with homology to the human transcription factor E4BP4 were confirmed by Northern blot analysis to be induced 10-20-fold by IL-4 treatment. This list of expressed genes in LPS + IL-4 treated B cells may shed further insight on the action and mechanism of IL-4 stimulation of cells.