Gene selection with multiple ordering criteria

Background  

A microarray study may select different differentially expressed gene sets because of different selection criteria. For example, the fold-change and p-value are two commonly known criteria to select differentially expressed genes under two experimental conditions. These two selection criteria often result in incompatible selected gene sets. Also, in a two-factor, say, treatment by time experiment, the investigator may be interested in one gene list that responds to both treatment and time effects.     

Culture-generated suppressor cells: evidence for an adherent cell component

Cells which suppress mixed lymphocyte reaction (MLR) and cytotoxic T-lymphocyte (CTL) generation can be demonstrated after culture for 3 to 5 days in the absence of added antigen. Such precultured suppressors are resistant to the cytotoxic effects of commercial rabbit anti-mouse brain serum, congenic anti-Thy-1.2 serum, and monoclonal anti-Thy-1.2 reagent. In addition, these cells, which adhere to both nylon wool and Sephadex G-10, ingest carbonyl iron. These properties suggest that precultured suppressors may not be thymus-processed. Precultured suppressor cells, when irradiated, are able to suppress only the MLR, and not the generation of allo-CTL. This finding, taken with our previously published work on the differential ontogeny of cells which suppress the MLR or CTL generation in culture, suggests that at least two kinds of suppressors are generated. One suppressor acts on CTL generation, is radiosensitive, and develops late in ontogeny; the other suppressor acts on proliferative cells in the MLR, is radioresistant, and develops early in ontogeny. Both kinds of suppressors, however, are adherent to nylon wool and Sephadex G-10, ingest carbonyl iron, and are resistant to anti-T-cell sera.     

The role of macrophages in B cell tolerance. I. Antigen-specific failure of Thy-1, Ly-2 negative adherent cells from tolerant mice to reconstitute immunocompetence in adherent cell deficient spleen cells

T-Cell-independent B-cell tolerance to the hapten derivatives of carboxymethyl cellulose (CMC) or methyl cellulose (MC) appears to be controlled by Thy-1-, Ly-2- adherent (A) cells contained in the spleen or peritoneal fluid. Immunocompetence in nonadherent (NA) normal spleen cells could be restored in vitro by irradiated A cells from normal mice. However, NA cells reconstituted with irradiated A cells derived from hapten specifically tolerant mice failed to respond to the same hapten, but responded normally to an immunogenic challenge with another unrelated antigen. A cells that had been preincubated at 4 degrees C with hapten derivatized MC also failed to restore immunocompetence. While preincubation of unfractionated spleen cells with the tolerogen under the same conditions resulted in B-cell unresponsiveness, such treatment of NA cells failed to render B cells tolerant. Treatment of A cells from tolerant mice with the reducing agent potassium iodide (KI) in vitro restored their capacity to render cultures of NA cells immunocompetent to the relevant hapten. Moreover, treatment with KI of spleen cells from mice injected with the tolerogen was shown to render them responsive. We suggest that B-cell tolerance induced by hapten derivatives of CMC and MC is mediated by suppressive macrophages contained among A cells. Certain subpopulations of macrophages are known to exert cytotoxic effects upon target cells by the release at close range of oxidating agents. We postulate that hapten derivatized CMC and MC, through unique properties of the carrier, bind to and possibly activate macrophages rendering them specifically suppressive for hapten binding B cells.     

Surrogate light chain-mediated interaction of a soluble pre-B cell receptor with adherent cell lines.

Signals initiated by the precursor B cell receptor (pre-BCR) are critical for B cell progenitors to mature into precursor B cells. The pre-BCR consists of a homodimer of microH chains, the covalently associated surrogate L (SL) chain composed of VpreB and lambda5, and the transmembrane signal molecules Ig(alpha) and Igbeta. One way to explain how maturation signals are initiated in late progenitor B cells is that the pre-BCR is transported to the cell surface and interacts from there with a ligand on stroma cells. To address this hypothesis, we first produced soluble Fab-like pre-BCR and BCR fragments, as well as SL chain, in baculovirus-infected insect cells. Flow cytometry revealed that, in contrast to Fab-like BCR fragments, the soluble pre-BCR binds to the surface of stroma and several other adherent cell lines, but not to B and T lymphoid suspension cells. The specific binding of the soluble pre-BCR to stroma cells is saturable, sensitive to trypsin digestion, and not dependent on bivalent cations. The binding of pre-BCR seems to be independent of the H chain of IgM (microH chain), because SL chain alone was able to interact with stroma cells. Finally, soluble pre-BCR specifically precipitated a 135-kDa protein from ST2 cells. These findings not only demonstrate for the first time the capacity of a pre-BCR to specifically bind to a structure on the surface of adherent cells, but also suggest that the pre-BCR interacts via its SL chain with a putative ligand on stroma cells.     

Experimental apparatus for selection of adherent microorganisms under stringent growth conditions.

A bioreactor apparatus is described for studying bacterial attachment. A cyclic, on-off, flow regime was imposed within the apparatus. Model calculations illustrate the utility of this flow pattern in the selection and maintenance of slow-growing, adherent organisms. The apparatus is believed to have general utility in testing bacterial attachment influenced by many types of experimental or environmental constraints, including variations in fluid dynamics, presence of toxic substances (metals or organics), nature of the substratum surface, concentrations of limiting nutrients, and competition between bacterial strains. As an example application, the apparatus was employed to test 14 bacterial strains for surface attachment in a nutrient-limited growth medium. The medium was developed, using the chemical equilibrium program MINEQL, for planned studies of biofilms in a solution with a chemically defined composition that permits calculation of trace metal speciation. The apparatus was used to select organisms with growth and attachment characteristics that could not be evaluated by conventional batch, or chemostat, culture conditions. When supplied with acetate, pyruvate, or succinate as a carbon and energy source, the gram-negative strains Pseudomonas cepacia 17616 and Zoogloea sp. WGO4 showed superior attachment characteristics to glass surfaces in the chemically defined medium but only moderate fluid-phase growth. The gram-positive Arthrobacter sp. strain 9G4D and gram-negative species P. pickettii and Zoogloea sp. WNJ8, when supplied with pyruvate as a carbon and energy source, were capable of superior growth in the fluid phase but formed only a low to moderate biofilm surface coverage.     

Bead transfection of adherent cells

Bead transfection is a simple, rapid, efficient, and cost-effective method of gene transfer into adherent mammalian cells. It involves a brief incubation of the cells with glass beads in a solution containing the DNA to be transferred. We have optimized this technique using COS-7 (an SV40 transformed monkey kidney cell line) and a transient expression assay for chloramphenicol acetyl transferase (CAT). Stable transfection efficiency assessed using the selectable marker gene neomycin phosphotransferase (NEO^R) was 27% in COS-7 cells. As this technique delivers high transfection efficiency with little manipulation of the exogenous DNA and does not require the use of any viral sequences, it may be a useful alternative method of gene delivery in the development of gene therapy protocols.     

Ion channels involved in cell volume regulation: effects on migration, proliferation, and programmed cell death in non adherent EAT cells and adherent ELA cells

This mini review outlines studies of cell volume regulation in two closely related mammalian cell lines: nonadherent Ehrlich ascites tumour cells (EATC) and adherent Ehrlich Lettre ascites (ELA) cells. Focus is on the regulatory volume decrease (RVD) that occurs after cell swelling, the volume regulatory ion channels involved, and the mechanisms (cellular signalling pathways) that regulate these channels. Finally, I shall also briefly review current investigations in these two cell lines that focuses on how changes in cell volume can regulate cell functions such as cell migration, proliferation, and programmed cell death.     

A genetic selection method for expression products that induce apoptosis in adherent mammalian cell lines

The process of apoptosis is carefully controlled in cells, and different cell types display different sensitivities to pro-apoptotic stimuli. The prospect of exploiting such differences for treatment of diseases such as cancer, via novel therapeutic agents, is extremely attractive. Therefore, genetic selections for novel expression products that kill cells may have considerable value. However, such selections are difficult to devise and perform because the selected cells do not grow. We developed a selection scheme designed to enrich for genetic agents that kill cells. The selection is based on detachment of apoptotic cultured mammalian cells from adherent monolayers. We characterized the properties of these detached cells (floating cells), and various aspects of the selection process. This selection method is potentially applicable to many mammalian cell lines.     

Electroporation-induced formation of individual calcium entry sites in the cell body and processes of adherent cells.

Electroporation is a widely used method for introducing macromolecules into cells. We developed an electroporation device that requires only 1 microl of sample to load adherent cells in a 10-mm2 surface area while retaining greater than 90% cell survivability. To better understand this device, field-induced permeabilization of adherent rat basophilic leukemia and neocortical neuroblastoma cells was investigated by using fluorescent calcium and voltage indicators. Rectangular field pulses led to the formation of only a few calcium entry sites, preferentially in the hyperpolarized parts of the cell body and processes. Individual entry sites were formed at the same locations when field pulses were repeated. Before calcium entry, a partial breakdown of the membrane potential was observed in both polar regions. Based on our results, a model is proposed for the formation and closure of macromolecule entry sites in adherent cells. First, the rapid formation of a large number of small pores leads to a partial membrane potential breakdown in both polar regions of the cell. Second, over tens of milliseconds, a few entry sites for macromolecules are formed, preferentially in the hyperpolarized part of cell body and processes, at locations defined by the local membrane structure. These entry sites reseal on a time scale of 50 ms to several seconds, with residual small pores remaining open for several minutes.     

Inhibition of murine lymphokine-activated killer (LAK) cell activity by adherent cells

The effects of adherent cell depletion, indomethacin, and prostaglandin E2 (PGE2) on murine LAK cell activity were investigated. Removal of plastic adherent cells from splenocyte suspensions either prior to 5-day culture with 1000 U/ml of recombinant human IL-2 (rIL-2) or prior to assay resulted in an enhanced LAK cell cytotoxicity compared to that of whole spleen cell suspensions. Indomethacin enhanced LAK cell cytotoxicity of whole splenocyte suspensions if present during the culture period, but had no effect on whole splenocyte or adherent cell-depleted cell suspensions if added just prior to assay. PGE2 suppressed LAK cell activity of nonadherent splenocyte but not whole splenocyte suspensions when present during the culture period. In vivo treatment of mice with indomethacin enhanced cytotoxicity directed toward both LAK sensitive, natural killer (NK) resistant (P-815) and LAK, NK sensitive (YAC-1) tumor cell targets. Splenocytes from indomethacin-treated mice cultured with additional indomethacin and rIL-2 exhibited highest LAK cell activity. The results from this study indicate that LAK cells are regulated by adherent cells which suppress LAK cell activity. This suppression can be reversed both in vitro and in vivo by indomethacin. This study has important implications for the possible clinical use of indomethacin in the potentiation of in vivo and in vitro LAK cell activity for immunotherapeutic protocols.     

Electroporation of adherent cells in situ

A simple, rapid, and reproducible procedure for the introduction of macromolecules into adherent mammalian cells by electroporation is described. Cells were growing on a glass surface coated with electrically conductive, optically transparent indium-tin oxide at the time of pulse delivery. Several factors affected the optimal voltage for permeation of a given line including the metabolic state of the cells and their degree of spreading onto the conductive growth surface. Careful control of the electric field strength resulted in almost 100% of the cells containing introduced antibodies without any detectable change in the length of their division cycle. Higher voltages were required for the stable expression of DNA than for the introduction of antibodies, resulting in a significant rate of cell death.     

Effects of isolated tumor lymphocytes alone and with adherent cells

Summary The effect on the growth of gradient-isolated mouse mammary tumor cells of different populations of lymphoid cells were evaluated in micrototoxicity assays. Variable effects were obtained with tumor-bearer lymph node and spleen cells: in some experiments growth stimulation occurred, whereas in others inhibition was observed. Mixed effector populations gave more regular results: adherent spleen cells added to lymph node or spleen lymphocytes inhibited tumor cell growth in six of nine experiments; inhibition occurred when either of the effector populations in the mixture was derived from the tumor-bearing mouse. Tumor-associated lymphoid cells (TAL) stimulated growth of the tumor cells in five of seven experiments. However, TAL inhibited tumor growth when combined with adherent spleen cells from tumor-bearing animals. In contrast with the peripheral lymphoid cells, admixture of control adherent cells from normal animals with TAL did not inhibit growth. No natural killer effect was seen in these growth inhibition assays. These data indicate that lymphoid populations capable of inhibiting tumor cell growth can be found in tumor-bearing animals, but such combination of active cells are not present at the tumor site.