A new genotoxicity assay based on p53 target gene induction.

The p53 tumor suppressor protein has emerged as a universal sensor of genotoxic stress that regulates the transcription of numerous genes required for appropriate cellular response to DNA damage. Therefore, transcriptional induction of p53 target genes can be considered as a global and early indicator of genotoxic stress. By performing expression microarrays and RNA-Seq analysis on wild-type and mutant TP53 human lymphocytes respectively derived from controls and Li-Fraumeni patients and exposed to different classes of genotoxic agents, we first determined a common p53-dependent transcriptional signature of DNA damage. We then derived a simple and fast assay based on the exposure of wild-type TP53 lymphocytes to physical or chemical agents and on the quantitative measurement of selected p53 target gene transcriptional induction. The specificity of the p53 genotoxicity assay can easily be demonstrated by performing the same experiment in control lymphocytes with heterozygous TP53 mutations, which compromise responses to DNA damage. This assay allowed us to show that most of the drugs commonly used in cancer treatment, except the microtubule poisons, are highly genotoxic. The p53 genotoxicity assay should facilitate the measurement of the genotoxic effects of chemical and physical agents and the identification of drugs that are not genotoxic and do not expose patients to the risk of secondary malignancies, especially those with a constitutional defect in response to DNA damage, such as patients with Li-Fraumeni syndrome.

Detection of environmental mutagens using the FACIM assay.

A genetically engineered diploid yeast strain named yJC2, was specifically developed for environmental mutagen detection and characterization of induced mutations. This strain contains one copy of the human TP53 tumour suppressor gene coding sequence which is used as a molecular target for mutagens and two copies of the ADE2 reporter gene allowing accurate measurement of the TP53 transcriptional activity. The strain sensitivity to mutagens was evaluated by exposing cells to UVC, 4-nitroquinoline (NQO) or to an organic extract of sediment from the Seine estuary. For all studied mutagens, a significant and dose-dependent increase of mutant frequency was observed. The present assay named FACIM II (Functional Analysis of Chemical-Induced TP53 Mutations) is more convenient than the FACIM I and more inducible than the SOS Chromotest to detect direct-acting mutagens in the environment.

Functional analysis of chemically-induced mutations at the flounder TP53 locus, the FACIM assay.

A functional assay was developed in yeast to identify mutations induced by DNA-damaging agents at the flounder TP53 locus. This assay named FACIM for functional analysis of chemically-induced p53 mutations, is based on the assumption that most genotoxin-induced mutations inactivate transcriptional activity of the TP53 protein. The functional status of the protein expressed in yeast was measured using a p53-responsive reporter gene. The FACIM assay was used to evaluate the mutagenesis of the flounder TP53 exposed in vitro to benzo[a]pyrene diol epoxide (BPDE). A dose-dependent increase of p53 mutation rate was observed with increasing concentrations of BPDE and extension of exposure time. Flounder TP53 gene appeared highly sensitive to point mutations since most of those identified targeted different nucleotides. Mutated base-pairs corresponded predominantly to guanines located on the non-transcribed strand of the DNA. The general distribution of mutations along the flounder TP53 protein was different from that identified in the human homologue suggesting species-differences in mutagenesis of the TP53 gene. Most of flounder TP53 mutants were defective for transactivation and cell growth regulation but some maintained a partial wild-type phenotype. This functional assay in yeast could be used for both evaluation of the genotoxic potency of chemicals or environmental samples and screening of p53 mutations in fish tumours.

The European flounder (Platichthys flesus) TP53 functions as a temperature-sensitive transcription factor which inhibits cell growth in yeast.

Numerous studies focus on biological roles of the TP53 tumor suppressor gene in mammals but little is known about the actual function of TP53 in lower vertebrates. In this study, we used an in vivo functional assay in yeast to address the transactivation capacity of the flounder TP53 protein. We showed that the flounder TP53 acts as a sequence-specific transcription factor which is able to transactivate various human promoters containing a p53-responsive element (RE). This transcriptional activity was completely abrogated in the Val147Glu TP53 mutant previously identified in two flounder hepatic hyperplasia. In addition, we showed that the wild-type (wt) flounder TP53 but not the Val147Glu mutant inhibits cell growth when expressed in yeast. We finally reported that transcription regulation and growth inhibition by the wild-type flounder TP53 is temperature-dependent. The flounder TP53 optimal temperature appeared lower than those reported for the Xenopus and human homologues.

Pescadillo, a novel cell cycle regulatory protein abnormally expressed in malignant cells.

Using a culture model of glial tumorigenesis, we identified a novel gene that was up-regulated in malignant mouse astrocytes following the loss of p53. The gene represents the murine homologue of pescadillo, an uncharacterized gene that is essential for embryonic development in zebrafish. Pescadillo is a strongly conserved gene containing unique structural motifs such as a BRCA1 C-terminal domain, clusters of acidic amino acids and consensus motifs for post-translational modification by SUMO-1. Pescadillo displayed a distinct spatial and temporal pattern of gene expression during brain development, being detected in neural progenitor cells and postmitotic neurons. Although it is not expressed in differentiated astrocytes in vivo, the pescadillo protein is dramatically elevated in malignant human astrocytomas. Yeast strains harboring temperature-sensitive mutations in the pescadillo gene were arrested in either G(1) or G(2) when grown in nonpermissive conditions, demonstrating that pescadillo is an essential gene in yeast and is required for cell cycle progression. Consistent with the latter finding, DNA synthesis was only observed in mammalian cells expressing the pescadillo protein. These results suggest that pescadillo plays a crucial role in cell proliferation and may be necessary for oncogenic transformation and tumor progression.

Cloning, expression, and characterization of DNA polymerase I from the hyperthermophilic archaea Thermococcus fumicolans.

The DNA polymerase I gene of a newly described deep-sea hydrothermal vent Archaea species, Thermococcus fumicolans, from IFREMERS's collection of hyperthermophiles has been cloned in Escherichia coli. As in Thermococcus litoralis, the gene is split by two intervening sequences (IVS) encoding inteins inserted in sites A and C of family B DNA polymerases. The entire DNA polymerase gene, containing both inteins, was expressed at 30 degrees C in E. coli strain BL21(DE3)pLysS using the pARHS2 expression vector. The native polypeptide precursor of 170kDa was obtained, and intein splicing as well as ligation of the three exteins was observed in vitro after heat exposure. The recombinant enzyme was purified and some of its activities were characterized: polymerization, thermostability, exonuclease activities, and fidelity.

High frequency in esophageal cancers of p53 alterations inactivating the regulation of genes involved in cell cycle and apoptosis.

Somatic mutations of the tumor suppressor gene p53 have been frequently detected in esophagal cancers, but their biological significance remains to be established. The tumor suppressor activity of p53 results in part from its ability to transactivate genes involved in the cell cycle and apoptosis, such as p21, bax and PIG3, and some p53 mutations may have a differential effect on the transactivation of these target genes. We developed yeast strains in which the activation by wild-type p53 of reporter plasmids containing p53 binding sites present within these target genes induces a change in the color of the colonies (red/white). Using these strains, we analyzed 56 esophageal cancers from patients residing in Normandy, France, a high incidence geographic area. Forty-seven tumors (84%), scored as mutant with the p21, bax and PIG3 reporter strains and in most of the cases (76%), the percentage of red colonies suggested that both p53 alleles were inactivated. Sequencing analysis allowed the identification of a p53 mutation in each positive sample, and the spectrum of mutations was in agreement with the etiological role of tobacco and alcohol. These results confirm the high frequency of biallelic p53 mutations in esophageal carcinoma and strongly suggest that their biological consequence is the complete alteration of the transactivation of genes involved in the cell cycle and apoptosis, which indicates that p53 alteration is a key event in esophagus carcinogenesis.

p53 mutations in bladder tumors inactivate the transactivation of the p21 and Bax genes, and have a predictive value for the clinical outcome after bacillus Calmette-Guerin therapy.

PURPOSE: We analyze the relationship among p53 mutations, p21 and Bax activation as well as their clinical implication in clinical response to intravesical bacillus Calmette-Guerin (BCG) therapy in high grade bladder tumors. MATERIALS AND METHODS: We analyzed a prospective series of 60 superficial bladder tumors using functional assays in yeast which test the transcriptional competence of p53 and can be used to identify p21 and Bax status. BCG instillations were given after initial tumor resection to 26 patients with a high risk of bladder invasive disease (pT1G3 tumors in 24 and carcinoma in situ in 2). RESULTS: No p53 alteration was detected in cases of pTa tumors. In contrast, p53 mutations were detected in 16 of 24 patients (66%) with pT1 G3 tumors and in 2 with primary carcinoma in situ. These 18 mutant samples scored also mutant for transactivation of p21 and Bax reporter strain. In 26 bladder tumors treated with BCG instillations there was a statistical difference (p = 0.0075) in the response to BCG therapy between 18 tumors with and 8 without alterations using functional assays in yeast. CONCLUSIONS: The p53 mutations, using functional assay in yeast, inactivate the transcription of p21 and Bax genes, and based on these preliminary results could have a useful predictive value for BCG therapy response in bladder cancer.

Selective detection of inactivating mutations of the tumor suppressor gene p53 in bladder tumors.

OBJECTIVE: Mutations in the p53 gene are implicated in the pathogenesis of half of all human tumors. In bladder tumors they are usually detected by immunohistochemistry. The assumption underlying protein analysis is that high level p53 expression is a consequence of mutations, but numerous exceptions have been reported. We describe the detection of p53 mutations in bladder cancer using a functional assay in yeast. MATERIALS AND METHODS: The prospective study consisted of 60 consecutive patients with bladder tumors (7 pT0, 2 CIS, 23 pTa, 24 pT1 and 4 pT2). High grade 3 was observed in primary carcinoma in situ, in 75% of pT1 tumors and in all pT2 tumors. The p53 mRNA extracted from endoscopic resection tissue was reverse transcribed and PCR-amplified. The transcriptional competence of the p53 cDNA was then tested in a yeast reporter strain. A simple functional assay was developed for p53 mutation in which human p53 is expressed in Saccharomyces cerevisiae which activates transcription of the ADE2 gene. Colonies containing wild type p53 are white and colonies containing mutant p53 are red. RESULTS: As this assay evaluates the critical biological function of p53, it can distinguish inactivating mutations from functionally silent mutations. In pTo and pTa bladder tumors, no p53 mutations were detected. In contrast, the functional assay permitted us to detect p53 mutations in 66% of patients with stage T1 tumors (72% of case of high grade 3) and in all cases with primary carcinoma in situ and in 4 cases of stage T2 tumors. CONCLUSION: This preliminary study demonstrates that this functional assay method is a simple and efficient procedure to detect p53 mutations in bladder cancers and suggests that p53 mutations seem to be associated with invasive bladder tumors.

Functional analysis of the p53 protein in AIDS-related non-Hodgkin's lymphomas and polymorphic lymphoproliferations.

Alteration of the tumour suppressor gene p53 is frequent in AIDS-related non-Hodgkin's lymphomas (AIDS-NHL), particularly in Burkitt's or Burkitt's-like lymphomas (BL/BLL). Since mechanisms of inactivation other than mutations have been advanced, the transcriptional activity of the p53 protein was studied in a functional assay in yeast in a series of AIDS-NHL lesions and compared with their morphology, immunohistochemistry (IHC) and single-strand conformation polymorphism (SSCP) analysis detection of other p53 abnormalities, Epstein-Barr virus (EBV) status, MDM-2 oncoprotein expression and c-MYC rearrangement. Polymorphic lymphoproliferations (PL), identified as precursors of NHL in HIV-patients, were also analysed in attempt to detect p53 modifications related to clonal progression. The functional assay detected p53 mutants in 40% (12/ 30) of the tumours: 50% (6/12) of BL/BLL, 40% (4/10) of diffuse large cell lymphomas (DLCL) and 25% (2/8) of PL. An oligoclonal or monoclonal population was identified in the two PL cases with mutant p53. An accumulation of the p53 protein was detected by IHC in 26% (8/30) of the tumours (five BL/BLL and three DLCL) and was associated with positive functional assay. In the 20 lesions tested by both of the screening methods for mutations, a p53 mutant pattern was detected in 55% of cases (11/20) and in 25% of cases (5/ 20) respectively with the functional assay and SSCP analysis of exons 5-8. There was no inverse correlation between the detection of EBV genome and the presence of p53 mutations and no overexpression of MDM-2 protein for the whole series. In conclusion, the functional assay was more sensitive than IHC and SSCP for the detection of p53 mutations in tumour samples. The mutations identified in AIDS-NHL lesions inactivate the p53 protein and in PL they could represent a selection of an aggressive clone.

Identification of human p53 mutations with differential effects on the bax and p21 promoters using functional assays in yeast.

Recent studies have suggested that a rare class of p53 mutants found in tumours has a subtle transcriptional defect affecting bax induction but not p21 induction. We have therefore developed simple functional assays in yeast which can be used to identify these mutants. Analysis of 51 different mutations observed in human tumours showed that all mutants tested scored as mutant with the bax reporter strain but nine scored as wild-type with the p21 reporter strain. These results, which can be explained by the lower affinity of the p53 protein for the bax site, may suggest that p21 is not the key target of p53 mutations in tumours. Since p21 status has recently been shown to modulate the chemotherapeutic and radiotherapeutic sensitivities of cancerous cells, the functional assays described here may have important clinical implications.

Field cancerisation and polyclonal p53 mutation in the upper aero-digestive tract.

Field cancerisation of the aerodigestive tract is caused by chronic exposure to alcohol and tobacco, but the nature of the genetic alterations preceding overt malignancy is unknown. To identify potential field changes we have used a functional assay which tests the transcriptional competence of human p53 expressed in yeast. To increase the sensitivity and reliability of the technique for samples containing under 20% mutant p53, the 5' and 3'-ends of the p53 cDNA were examined separately. With this split form of the assay the tissue p53 mRNA acts as its own control for RNA quality. Mutations were detected in 87% (46/53) of tumours, reflecting the high sensitivity of the technique. Multiple biopsies of histologically normal tissue from the upper aero-digestive tract were tested and clonal p53 mutations were identified in 76% (38/50) of biopsies from patients presenting with multiple tumours compared with 32% (38/117) of biopsies from patients presenting with single tumours (P<0.000001). All patients (16/16) presenting with multiple tumours had at least one positive biopsy, compared with only 53% (19/36) of patients presenting with single tumours (P <0.001). This defines expansion of multiple clones of mutant p53-containing cells as an important biological mechanism of field cancerisation, and provides a means to identify patients likely to benefit from intensive screening for the development of new head and neck tumours.

The human tumour suppressor gene p53 is alternatively spliced in normal cells.

Alternative splicing affecting the p53 carboxy-terminus has previously been described in mouse but not in normal human cells. We report here the detection in normal human lymphocytes of an alternatively spliced form of human p53 mRNA containing an additional 133 bp exon derived from intron 9. This splice variant encodes a truncated protein of 341 amino-acids including 10 new amino-acids derived from the novel exon. The truncated protein, which lacks part of the p53 tetramerization domain, fails to bind DNA in vitro and has a transcriptional defect in vivo in both yeast and mammalian cells. Quantitative RT-PCR experiments suggest that the alternatively spliced form is only present in significant amounts in quiescent cells. Considering the numerous functions ascribed to the carboxy-terminus of the p53 protein, this splice variant may have important implications for the biological role of p53 in normal cells.

Mutations of the presenilin I gene in families with early-onset Alzheimer's disease.

We analyzed 12 families with autosomal dominant early-onset Alzheimer' s disease (EOAD)for mutations in the coding region of the presenilin I (PSNLI) gene corresponding to the AD3 locus on chromosome 14q24.3. A total of eight missense mutations at codons 82, 115, 139, 163, 231, 264, 392, and 410 including six novel mutations, were identified in eight families. Cosegregation of the mutations with EOAD was confirmed in three families, one including 36 affected individuals. This study underlines the great allelic heterogeneity and the large distribution of the mutations within the PSNLI coding region. Our results support the notion that PSNLI is the major gene involved in autosomal dominant EOAD.

A simple p53 functional assay for screening cell lines, blood, and tumors.

Mutations in the p53 gene are implicated in the pathogenesis of half of all human tumors. We have developed a simple functional assay for p53 mutation in which human p53 expressed in Saccharomyces cerevisiae activates transcription of the ADE2 gene. Consequently, yeast colonies containing wild-type p53 are white and colonies containing mutant p53 are red. Since this assay tests the critical biological function of p53, it can distinguish inactivating mutations from functionally silent mutations. By combining this approach with gap repair techniques in which unpurified p53 reverse transcription-PCR products are cloned by homologous recombination in vivo it is possible to screen large numbers of samples and multiple clones per sample for biologically important mutations. This means that mutations can be detected in tumor specimens contaminated with large amounts of normal tissue. In addition, the assay detects temperature-sensitive mutants, which give pink colonies. We show here that this form of p53 functional assay can be used rapidly to detect germline mutations in blood samples, somatic mutations in tumors, and mutations in cell lines.

The NACP/synuclein gene: chromosomal assignment and screening for alterations in Alzheimer disease.

The major component of the vascular and plaque amyloid deposits in Alzheimer disease is the amyloid beta peptide (A beta). A second intrinsic component of amyloid, the NAC (non-A beta component of amyloid) peptide, has recently been identified, and its precursor protein was named NACP. A computer homology search allowed us to establish that the human NACP gene was homologous to the rat synuclein gene. We mapped the NACP/synuclein gene to chromosome 4 and cloned three alternatively spliced transcripts in lymphocytes derived from a normal subject. We analyzed by RT-PCR and direct sequencing the entire coding region of the NACP/synuclein gene in a group of patients with familial early onset Alzheimer disease. No mutation was found in 26 unrelated patients. Further studies are required to investigate the implication of the NACP/synuclein gene in Alzheimer disease.

Quenching of the tyrosyl free radical of ribonucleotide reductase by nitric oxide. Relationship to cytostasis induced in tumor cells by cytotoxic macrophages.

Nitric oxide (NO) synthesized by macrophages inhibits tumor cell replication. NO also inhibits ribonucleotide reductase, an enzyme essential for DNA synthesis, probably by quenching the catalytically active tyrosyl free radical of its R2 subunit. The role of this inhibition in NO-mediated cytostasis was thus evaluated. After a 4-h coculture with macrophages, quenching of the radical was demonstrated by electron paramagnetic resonance spectroscopy in transfected L1210-R2 cells over-expressing the R2 protein. Pronounced cytostasis was simultaneously observed. A NO synthase inhibitor greatly reduced both phenomena. Target cells withdrawn from macrophages partially recovered from cytostasis and radical loss within 90 min. Deoxyribonucleosides added to by-pass ribonucleotide reductase inhibition efficiently reversed cytostasis of K-562 cells. After a 24-h coculture, the quenched tyrosyl radical still reappeared in L1210-R2 cells withdrawn from macrophages, but DNA synthesis did not resume. Moreover, deoxyribonucleosides marginally reversed overnight cytostasis of K-562 cells mediated by macrophages but were efficient against cytostasis induced by hydroxyurea, a ribonucleotide reductase inhibitor. Autocrine cytostasis observed early in TA3-H2 cells committed to produce NO was closely correlated with quenching of the tyrosyl radical but not with formation of dinitrosyl-iron complexes. We thus propose that NO-dependent cytostasis begins with a rapid and reversible inhibition of ribonucleotide reductase, progressively reinforced by other, long-lasting antiproliferative effects.

Early loss of the tyrosyl radical in ribonucleotide reductase of adenocarcinoma cells producing nitric oxide.

Nitric oxide (NO) has been previously shown to inhibit crude preparations of ribonucleotide reductase, a key enzyme in DNA synthesis, and to destroy the essential tyrosyl free radical in pure recombinant R2 subunit of the enzyme. In R2-overexpressing TA3 cells, a decrease in the tyrosyl radical was observed by whole-cell EPR spectroscopy, as soon as 4 h after NO synthase induction by immunological stimuli. Complete loss of the tyrosyl EPR signal occurred after 7 h in cells cultured at a high density. Disappearance of the tyrosyl radical was prevented by N omega-nitro-L-arginine, a specific inhibitor of NO synthesis, and by oxyhemoglobin, which reacts rapidly with NO. It was reproduced by S-nitrosoglutathione, a NO-releasing molecule. Stable end products of NO synthase metabolism did not affect the radical. Immunoblot analysis of the R2 subunit indicated that expression of the protein was not influenced by NO synthase activity. These results establish that NO, or a labile product of NO synthase, induces the disappearance of the R2-centered tyrosyl radical. Since the radical is necessary for ribonucleotide reductase activity, its destruction by NO would contribute markedly to the antiproliferative action exerted by macrophage-type NO synthase.