Putative dehydrogenase tms1 suppresses growth arrest induced by a p53 tumour mutant in fission yeast

Differential prioritization between relevance and redundancy in correlation-based feature selection techniques for multiclass gene expression data

BACKGROUND

Due to the large number of genes in a typical microarray dataset, feature selection looks set to play an important role in reducing noise and computational cost in gene expression-based tissue classification while improving accuracy at the same time. Surprisingly, this does not appear to be the case for all multiclass microarray datasets. The reason is that many feature selection techniques applied on microarray datasets are either rank-based and hence do not take into account correlations between genes, or are wrapper-based, which require high computational cost, and often yield difficult-to-reproduce results. In studies where correlations between genes are considered, attempts to establish the merit of the proposed techniques are hampered by evaluation procedures which are less than meticulous, resulting in overly optimistic estimates of accuracy.

RESULTS

We present two realistically evaluated correlation-based feature selection techniques which incorporate, in addition to the two existing criteria involved in forming a predictor set (relevance and redundancy), a third criterion called the degree of differential prioritization (DDP). DDP functions as a parameter to strike the balance between relevance and redundancy, providing our techniques with the novel ability to differentially prioritize the optimization of relevance against redundancy (and vice versa). This ability proves useful in producing optimal classification accuracy while using reasonably small predictor set sizes for nine well-known multiclass microarray datasets.

CONCLUSION

For multiclass microarray datasets, especially the GCM and NCI60 datasets, DDP enables our filter-based techniques to produce accuracies better than those reported in previous studies which employed similarly realistic evaluation procedures.

The GRIMs: a new interface between cell death regulation and interferon/retinoid induced growth suppression

Cytokines and vitamins play a central role in controlling neoplastic cell growth. The interferon (IFN) family of cytokines regulates antiviral, anti-tumor, antimicrobial, differentiation, and immune responses in mammals. Significant advances have been made with respect to IFN-induced signal transduction pathways and antiviral responses. However, the IFN-induced anti-tumor actions are poorly defined. Although IFNs themselves inhibit tumor growth, combination of IFNs with retinoids (a class of Vitamin A related compounds) strongly potentiates the IFN-regulated anti-tumor action in a number of cell types. To define the molecular mechanisms involved in IFN/retinoid (RA)-induced apoptosis we have employed a genetic approach and identified several critical genes. In this review, I provide the current picture of IFN- RA- and IFN/RA-regulated growth suppressive pathways. In particular, I focus on a novel set of genes, the genes-associated with retinoid-interferon induced mortality (GRIM). GRIMs may be novel types of tumor suppressors, useful as biological response markers and potentially novel targets for drug development.

Mutational analysis of human thioredoxin reductase 1. Effects on p53-mediated gene expression and interferon and retinoic acid-induced cell death

The interferon (IFN)-beta and all-trans-retinoic acid combination suppresses tumor growth by inducing apoptosis in several tumor cell lines. A genetic technique permitted the isolation of human thioredoxin reductase (TR) as a critical regulator of IFN/all-trans-retinoic acid-induced cell death. Our recent studies have shown that TR1:thioredoxin 1-regulated cell death is effected in part through the activation of p53-dependent responses. To understand its death regulatory function, we have performed a mutational analysis of TR. Human TR1 has three major structural domains, the FAD binding domain, the NADPH binding domain, and an interface domain (ID). Here, we show that the deletion of the C-terminal interface domain results in a constitutive activation of TR-dependent death responses and promotes p53-dependent gene expression. TR mutant without the ID still retains its dependence on thioredoxin for promoting these responses. Thus, our data suggest that TR-ID acts as a regulatory domain.

Modulation of p53 dependent gene expression and cell death through thioredoxin-thioredoxin reductase by the Interferon-Retinoid combination

We have shown earlier that the IFN-beta and all-trans retinoic acid (RA) combination, but not the single agents, induces death in several tumor cell lines. Employing a genetic technique we have identified several Genes associated with Retinoid-IFN induced Mortality (GRIM). One of the GRIMs was human thioredoxin reductase (TR), a redox enzyme. Since the overexpressed TR augments IFN/RA stimulated cell death, we explored the mechanisms of TR-mediated death. Here we show that TR augments cell death by upregulating the transcriptional activity of p53 tumor suppressor. This process does not involve a physical increase in levels of p53. Using redox inactive mutants of TR and its substrate, thioredoxin (Trx), we demonstrate that IFN/RA-induced regulation of p53 dependent gene expression requires TR and Trx. In contrast-over-expression of wildtype TR or Trx augment the p53 dependent gene expression in response to IFN/RA treatment. Consistent with these results an increased DNA binding activity of p53 was noted in the presence of TR. These studies identify a novel mechanism of p53 mediated cell death regulation involving redox enzymes.

Production and characterization of a rabbit monoclonal antibody against human CDC25C phosphatase

We produced a rabbit monoclonal antibody (MAb) against human CDC25C phosphatase. The antibody reacts with a minimal epitope between amino acids 291-295 in the highly conserved C-terminal region of CDC25C. The antibody recognizes denatured CDC25C of recombinant and mammalian origin in Western blot analysis. The corresponding rabbit polyclonal serum is able to immunoprecipitate the native protein, but this ability has been lost during the selection procedure. Although the production of the rabbit MAb requires more effort and patience than the mouse MAb technology, it offers a true alternative in case of antigens that are not immunogenic in mice.

Human p53 restores DNA synthesis control in fission yeast

The p53 gene is the most common target for genetic alterations in human cancers. As a transcriptional regulator p53 enhances the expression of proteins that control cellular proliferation. Although there is no evidence of a p53 homologous gene in yeast, the p53 protein was found to be functional in terms of growth repression and transactivation in yeast, suggesting that some features of p53 function are conserved. Here we report the construction and characterization of a p53 wild type expression strain of fission yeast. Upon induction of wild type p53 expression a dosage dependent growth arrest was observed rendering recipient yeast cells sensitive to UV irradiation in a p53 dosage dependent fashion. The observed growth arrest was efficiently suppressed by coexpression of human CDC25C phosphatase, which restored a normal resistance to UV irradiation in p53 and CDC25C coexpressing yeast cells. Furthermore, expression of CDC25C alone inactivated the DNA synthesis control whereas p53 and CDC25C coexpressing yeast cells showed an intact checkpoint control. Upon moderate expression of wild type p53 a restoration of the DNA synthesis control was also observed in a cdc2.3w mutant background, whereas a tumor mutant of p53 failed to restore this important checkpoint in fission yeast.

Phosphorylation mutants of p53 show differential complex formation with putative dehydrogenase Tms1 of fission yeast

The yeast tms1 gene was originally identified as a multi-copy suppressor of a lethal growth arrest caused by expression of a tumour mutant cDNA of p53 in fission yeast. The tms1 gene product (Tms1) was found to form stable complexes with p53 in yeast and in vitro; using purified recombinant proteins, the interaction was mapped to the C-terminal region of p53. This part is known to be modified by several protein kinases resulting in a transition of p53 from a latent to an activated state capable of transactivating various cellular genes involved in growth suppression or apoptosis. Since there is evidence for an evolutionary conservation of a Tms1-related protein in mammals, the effect of the phosphorylation status of the C-terminus of p53 on Tms1/p53 complex formation in vitro has been investigated. Whereas mutants changing the cdc2 phosphorylation site at position 315 of human p53 had only little effect on Tms1/p53 complex formation, we found that mutants involving the protein kinase CK2 site at position 392 showed a significantly decreased relative affinity for the Tms1 protein. The same result was obtained by using a C-terminal fragment of p53 which was phosphorylated by purified protein kinase CK2, suggesting that the complex formation of p53 with cellular C-terminal binding proteins like Tms1 impairs regulation by phosphorylation.

A mutation in a thioredoxin reductase homolog suppresses p53-induced growth inhibition in the fission yeast Schizosaccharomyces pombe

A strong growth inhibition is observed when the human p53 tumor suppressor gene product is expressed in the fission yeast Schizosaccharomyces pombe. This growth inhibition is specific for wild-type p53; mutant alleles of p53 derived from human tumors show a greatly decreased ability to inhibit growth. These data suggest that there may be a p53-responsive pathway in S. pombe. To identify elements in this pathway genetically, we isolated a mutant yeast strain in which the growth inhibitory activity of p53 is largely suppressed. In addition, the activity of p53 as a transcription factor is also decreased in this strain. The suppression of p53 activity is not due to a decrease in p53 expression or a failure of p53 to localize to the nucleus. This p53 suppressor mutation is in a novel S. pombe gene with homology to thioredoxin reductase genes, and has been named trr1. Strains with a mutation of, or deletion in, trr1 are sensitive to oxidizing agents, suggesting that the trr1 suppressor mutation causes partial loss of trr1 function. Since oxidizing agents are able to suppress p53 activity in vitro, this trr1 mutation may affect the activity of p53 in fission yeast by increasing the oxidation state of the tumor suppressor.

Precise mapping of the tms1 binding site on p53

Originally identified as multicopy suppressor of a lethal growth arrest caused by expression of a tumour mutant cDNA of p53 in fission yeast the tms1 gene product was found to form stable complexes with p53 in yeast. By using purified recombinant proteins multimeric complexes of tms1 and p53 could be demonstrated and recently the p53 binding site on the tms1 protein was established to the sequence YYITTEDFCT (aa 116-125) in the vicinity of a well conserved cell division motif. Here we report the precise mapping of the tms1 binding site on the p53 protein to the sequence LQIRGRERFE (aa 330-339) which defines a new functional domain on the p53 protein.

Precise epitope mapping of three monoclonal antibodies raised against tms1 protein of fission yeast

Recently we described the production of two monoclonal antibodies 10G2 and 10C4 of IgG3 subclass raised against the recombinant tms1 protein of fission yeast. Here we introduce a new monoclonal antibody 2E2 of IgG1 subclass and present the precise epitope mapping of these monoclonal antibodies using tms1 deletion mutants and synthetically produced oligopeptides spanning the tms1 protein by immunoblot analysis.

Isolation and characterization of two monoclonal antibodies raised against tms1 protein of fission yeast

Monoclonal antibodies were produced against recombinant tms1 protein of fission yeast. The antibodies of IgG3 subclass were isolated from serum-free cell culture medium and purified by affinity chromatography on protein A-Sepharose. The antibodies can be used to detect specifically the tms1 protein on immunoblots of total yeast lysates. In addition, native tms1 protein is specifically precipitated by these antibodies from yeast lysates.

The emerging picture of p53

1. The cellular phosphoprotein p53 is a negative regulator of the cell growth. A great majority of human malignancies expresses a mutated p53 that represents an oncogenic version of the protein. 2. However, in the meantime many tumors were identified containing a p53 protein without any mutation. Here also other events than genomic alterations of p53 might be implicated in the process of cell transformation. 3. The expression of wild-type or mutant conformation is not exclusively defined by the p53 DNA sequence but also influenced by the subcellular environment and the interaction of cellular proteins with p53. 4. In particular, the mdm-2 gene product appears to be an important partner of p53 somehow involved in these complex regulatory processes. 5. Recent findings supported a role for p53 in transcriptional regulation, perhaps by reducing the expression of genes that are needed for ongoing cell proliferation. 6. This property may be based upon the ability of p53 to bind DNA as well as different proteins from viral or cellular origin. 7. Especially transcription factors or further cellular proteins connected in any way with the regulation of cell proliferation are possible candidates. 8. Thus, it is not surprising that p53 is implicated in the regulation of the cell cycle and in the decision of a cell to replicate DNA or to go into apoptosis.