Sequence analysis and expression in cultured lymphocytes of the human FOSB gene (G0S3)

Metabolic optimization of adoptive T cell transfer cancer immunotherapy: A historical overview

After prolonged extracorporeal multiplication in physiological culture media, there can be curative infusions of a cancer patient's own cytotoxic T cells (adoptive T cell transfer; ACT), which must achieve efficient activation in potentially adverse tumour microenvironments. With spectacular, yet irregular, success, improvements are needed. Developing lymphoid cells are biologically selected, not only for 'near-self' reactivity (positive selection), but also to avoid self-reactivity (negative selection). Thus, success requires harnessing near-self cells while avoiding extreme autoimmune phenomena. Abrupt metabolic changes accompanying T cell activation to leave the G₀ stage and enter the G₁ stage of the cell cycle (eg enhanced glycolysis) are accompanied by increased transcription of the G0S9 gene that mediates salvage synthesis of NAD⁺ from nicotinamide; the latter has recently been shown to increase the efficiency of ACT. Despite theoretical and experimental advances, there has not been parallel progress in simulating in vivo conditions with culture media that were initially formulated for their positive benefits for tumour cell lines (cell survival and proliferation). Yet for lymphoid cells, inhibition or death (ie immunological tolerance) is as important as their activation and proliferation (immunological response). Thus, use of media optimized for the latter may mask the former. The resilience of established culture protocols may have been partly politically driven. However, unphysiological conditions have sometimes yielded fortuitous insights. Optimization of culture media for specific tissues must consider the nature of problems addressed in research settings and the need to avoid mishaps in clinical settings.

Two signal half-century: From negative selection of self-reactivity to positive selection of near-self-reactivity

With the emergence of clonal selection ideas in the 1950s, the development of immune cell repertoires was seen to require the negative selection of self-reacting cells, with surviving cells exhibiting a broad range of specificities. Thus, confronting a universe of not-self-antigens, a potential host organism spread its resources widely. In the 1960s, the two signal hypothesis showed how this might work. However, in the 1970s an affinity/avidity model further proposed that anticipating a pathogen strategy of exploiting "holes" in the repertoire created by negative selection, hosts should also positively select near-self-reacting cells. A microbe mutating an antigen from a form foreign to its host to a form resembling that host should prevail over host defences with respect to that antigen. By mutating a step towards host self, along the path from non-self to self, it should come to dominate the microbe population. By progressive stepwise mutations, such microbes would become better adapted, to the detriment of their hosts. But they would lose this advantage if, as they mutated closer to host self, they encountered progressively stiffer host defences. Thus, as described in the affinity/avidity model, positive selection of lymphocytes for specificities that were very close to, but not quite, anti-self (ie, "anti-near-self") should be an important host adaptation. While positive selection affects both B and T cells, mechanisms are uncertain. Converging evidence from studies of lymphocyte activation, either polyclonally (with lectins as "antigen-analogs") or monoclonally (by specific antigen), supports the original generic affinity/avidity model for countering mutations towards host self.

Forskolin and Phorbol 12-myristate 13-acetate modulates the expression pattern of AP-1 factors and cell cycle regulators in estrogen-responsive MCF-7 cells

Activator protein-1 (AP-1) transcription factor is a key component of many signal transduction pathways involved in the regulation of cellular processes and controls rapid responses of mammalian cells when exposed to the variety of stimulus. The phorbol 12-myristate 13-acetate and Forskolin (Fo) are well-known kinase activators/stimulators of Protein Kinase C (PKC) and Protein Kinase A (PKA) respectively. Importantly, these kinases are found to be present in transitional points of many cell signaling pathways, especially those involved in proliferation. The stimulating effect of PKC and PKA on the expression of AP-1 factors in MCF-7 breast cell proliferation is not well characterized. Hence, the role of PKC by PMA treatment and the role of PKA by using Fo in MCF-7 cells is investigated. Where, cells treated with PMA showed increased cell proliferation, while Fo had no effect, but inhibited the PMA induced proliferation. The RT-PCR results showed the PMA induced c-Jun, c-Fos and Fra-1 expressions compared to control and Fo. However, Fo in combination with PMA, inhibit the PMA induced above mRNA expressions where Fo alone has no effect. Western blot studies validated the c-Jun expressions in PMA treated MCF-7 cells. Further, PMA increases the mRNA expression of Cyclin-E1, Cyclin-D1, and CDK-4, whereas Fo decreases their expressions. Thus, mitogenic effect of PMA and inhibitory action of Fo on MCF-7 cells is probably enhanced via activation of AP-1 factors and concomitant action of cell cycle regulators in the downstream singling cascade.

Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues

The stability of a folded single-stranded nucleic acid depends on the composition and order of its constituent bases and may be assessed by taking into account the pairing energies of its constituent dinucleotides. To assess the possible biological significance of a computed structure, Maizel and coworkers in the 1980s compared the energy of folding of a natural single-stranded RNA sequence with the energies of several versions of the same sequence produced by shuffling base order. However, in the 2000s many took as self-evident the view that shuffling at the mononucleotide level (single bases) was conceptual wrong and should be replaced by shuffling at the level of dinucleotides (retaining pairs of adjacent bases). Folding energies then became indistinguishable from those of corresponding shuffled sequences and doubt was cast on the importance of secondary structures. Nevertheless, some continued productively to employ the single base shuffling approach, the justification for which is the topic of this paper. Because dinucleotide pairing energies are needed to calculate structure, it does not follow that shuffling should not disrupt dinucleotides. Base shuffling allows determination of the relative contributions of base composition and base order to total folding energy. The potential for secondary structure arises from pressures acting at both DNA and RNA levels, and is abundant throughout genomes-with a probable primary role in recombination. Within a gene the potential can often be accommodated, and base order and composition work together (values have the same negative sign) in contributing to total folding energy. But sometimes protein-coding pressure on base order conflicts with the pressure for secondary structure and the values have opposite signs. Total folding energy can be deemed of potential biological significance when the average of several readings is significantly less than zero.

FosB is highly expressed in normal mammary epithelia, but down-regulated in poorly differentiated breast carcinomas

FosB is a member of the AP-1 family of transcription factors which represent important regulators of cell proliferation and differentiation. Based on prior results which indicated a role of FosB in breast cancer, we studied FosB protein and mRNA expression by immunohistochemistry and, partly, in situ hybridization in 68 mammary carcinomas and normal breast tissues. We found strong nuclear FosB immunoreactivity in epithelial cells of normal lobules and ducts, whereas carcinomas frequently showed loss of FosB expression (n = 8) or weak immunostaining (n = 24). Reduced FosB protein expression in tumors correlated with high grading (p = 0.005), negative estrogen and progesterone receptor status (p < 0.001), and strong HER2/neu expression (p = 0.025). Comparison with expression of seven cell-cycle regulators revealed an association of low/absent FosB staining with p16MTS1 overexpression (p = 0.005). RT-PCR showed expression of full-length FosB and the smaller splice variant FosB2 in most carcinomas and cell lines with and without FosB protein expression, indicating that both proteins are differentially regulated mainly at a post-transcriptional level. By sequence analysis of the coding region in four cell lines and 17 carcinomas we detected a mutation in HBL-100 cells. Our results indicate that high FosB expression might be necessary for normal proliferation and differentiation of mammary epithelial cells, and reduced FosB protein levels might be involved in dedifferentiation during breast tumorigenesis.

Immunity as a function of the unicellular state: implications of emerging genomic data

Instead of being greeted as supporting the growing corpus of immunological theory, recent advances in the bioinformatic analysis of genomes have often surprised the discoverers and failed to attract the attention of immunologists. In fact, the view that multicellular immune systems are adaptations of already highly evolved unicellular immune systems that are capable of self/not-self discrimination can assist our comprehension of phenomena, such as 'junk' DNA, genetic polymorphism and the ubiquity of repetitive elements. For instance, the 'hidden transcriptome', revealed by run-on transcription of genes or repetitive elements, contains a diverse repertoire of RNA 'immune receptors' with the potential to form double-stranded RNA with viral RNA 'antigens', thus triggering intracellular alarms.

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.

Introns resolve the conflict between base order-dependent stem-loop potential and the encoding of RNA or protein: further evidence from overlapping genes

Many eukaryotic genes are split into exons and introns, the latter being removed post-transcriptionally so that only exon sequences appear in cytoplasmic RNAs. Since introns appear in both protein-encoding RNAs and non-protein-coding RNAs, they interrupt genetic information per se, not just protein-encoding information. A DNA sequence has the potential to carry more than one type of genetic information, but different types may conflict. Thus, it has been proposed that introns arose because sequences were unable to contain concomitantly complete information for the encoding both of stem-loops and of cytoplasmic products (protein and/or RNA). Stem-loop potential is held to be selectively advantageous since it promotes the recombination-dependent correction of genetic errors. Stem-loop potential, the best local measure of which is base order-dependent stem-loop potential, tends to be less in exons than in introns. This is particularly evident in genes evolving rapidly under positive Darwinian selection, where the protein-encoding function is dominant. Evidence is now presented that the rare regions where genes overlap also impose excessive encoding demands so that the concomitant coding of base order-dependent stem-loop potential is decreased. Our results are consistent with the hypothesis that sequences with high stem-loop potential arose in the early 'RNA world'. Ancestors of modern genes would have entered this world when sequences (exons) encoding cytoplasmic products, were interspersed with sequences (introns) encoding selectively advantageous stem-loops. Purine-loading pressure would also have favoured intron formation.

Chargaff's legacy

Of Chargaff's four rules on DNA base composition, only his first parity rule was incorporated into mainstream biology as the DNA double helix. Now, the cluster rule, the second parity rule, and the GC rule, reveal the multiple levels of information in our genomes and potential conflicts between them. In these terms we can understand how double-stranded RNA became an intracellular alarm signal, how potentially recombining nucleic acids can distinguish between 'self' and 'not-self' so leading to the origin of species, how isochores evolved to facilitate gene duplication, and how unlikely it is that any mutation can ever remain truly neutral.

Expression and processing of G0/G1 switch gene 24 (G0S24/TIS11/TTP/NUP475) RNA in cultured human blood mononuclear cells

The human G0/G1 switch (G0S) gene, G0S24, and its rodent immediate-early homolog (TIS11, TTP, NUP475) are part of a mammalian gene family whose members encode CCCH zinc finger domains and domains similar to part of the large subunit of RNA polymerase II and to the Mei2 regulator of G1 arrest in fission yeast. We compared the RNA expression of G0S24 with that of other G0S genes in cultured blood mononuclear cells and examined the levels of various RNA processing intermediates. Freshly isolated cells contained high levels of several G0S RNAs, which declined by 24 h, suggesting transient spontaneous stimulation during cell purification (Heximer et al., 1996). However, in cells preincubated for 24 h, G0S24 RNA levels remained much higher than those of other G0S genes (107+/-42 x 10(6) molecules/microg of RNA); stimulation with lectin (Con-A) further increased G0S24 RNA, much of which remained nuclear. Like those of FOS/G0S7, EGR1/G0S30 and of the gene encoding the regulator of G protein signalling 1 (RGS1), G0S24 RNA levels increased more in response to a protein kinase C activator than to a calcium ionophore, whereas the opposite held for FOSB/G0S3 and RGS2/G0S8. With appropriate PCR primer pairs, we showed a G0S24 RNA processing intermediate, which crossed the exon-1/intron boundary, and nonpolyadenylated nuclear RNA extending into the 3' flank, where there is a second CpG island. The concentration of the latter intermediate (1.2+/-0.2 x 10(6) molecules/microg of RNA), which increased transiently on cell stimulation, did not account for all G0S24 nuclear RNA. The levels of G0S24 RNA and both intermediates were increased by the protein synthesis inhibitor cycloheximide, consistent with regulation by a labile repressor.

Cyclosporin A inhibits early mRNA expression of G0/G1 switch gene 2 (G0S2) in cultured human blood mononuclear cells

Cyclosporin A (CsA) may achieve its immunosuppressive effects by inhibiting the calcium- and calmodulin-dependent phosphatase calcineurin which is required for activation of target genes by members of the NFAT (nuclear factor of activated T cells) transcription factor family. Among these target genes is the gene encoding interleukin-2 (IL2), a cytokine facilitating progression through the G1 phase of the cell cycle. However, IL2 does not reverse CsA inhibition, suggesting that at least one other NFAT-sensitive gene may be involved. The human G0/G1 switch gene, G0S2, has potential NFAT-binding sites in the 5' flank and encodes a small basic potential phosphoprotein of unknown function. Using a sensitive, reverse transcription-polymerase chain reaction (RT-PCR) assay, G0S2 mRNA levels were assayed in cultured blood mononuclear cells. Freshly isolated cells contain high levels of G0S2 mRNA which rapidly decline. This "spontaneous stimulation" is also noted with some other G0S genes and has been attributed to some aspect of the isolation procedure. In cells that have been preincubated to lower mRNA levels, there is a transient increase in G0S2 mRNA, peaking between 1-2 h, in response to Concanavalin-A (ConA), or to the combination of phorbol ester (TPA), and the calcium ionophore, ionomycin. Both these responses are inhibited by CsA. Our results suggest that G0S2 expression is required to commit cells to enter the G1 phase of the cell cycle, and that, while not excluding other possible targets, early inhibition of G0S2 expression by CsA may be important in achieving immunosuppression. G0S2 may be of value as a reporter gene for analyzing the mechanism of action of CsA and its influence on the positive and negative selection of lymphocytes in response to self and not-self antigens.

Comparison of mRNA expression of two regulators of G-protein signaling, RGS1/BL34/1R20 and RGS2/G0S8, in cultured human blood mononuclear cells

RGS1 and RGS2 are members of a new class of regulators of G-protein signaling identified by their selective mRNA expression either in phorbol ester (TPA)-stimulated human B lymphocytes (RGS1/1R20/BL34) or in blood mononuclear cells treated with the T-cell lectin concanavalin A (ConA) and cycloheximide (RGS2/G0S8). The RGS1 gene shows low basal mRNA expression in freshly purified blood mononuclear cells, which increases upon incubation for a day. In contrast, RGS2 initially shows high basal levels of mRNA expression, which subsequently decrease. Expression of both genes increases in response to ConA, with RGS2 mRNA levels increasing briskly to a maximum between 0.5 and 1 hr and decreasing to baseline by 6 hr, whereas the RGS1 mRNA increase is delayed reaching a maximum between 1 and 2 hr. RGS1 mRNA levels increase much more in response to a protein kinase C activator (TPA), than to a calcium ionophore (ionomycin), whereas the opposite is true for RGS2. We suggest that ConA elevates RGS2 on the basis of its ability to increase intracellular calcium, and that RGS2 may be involved in the regulation of intracellular calcium. The distinction between RGS1 and RGS2 is further emphasized by studies indicating that recombinant RGS2 does not bind in vitro to two members of the G(i) subfamily of G-protein alpha-subunits for which recombinant RGS1 has high affinity.