Germline mutations of the PTEN gene in Cowden disease, an inherited breast and thyroid cancer syndrome.

Cowden disease (CD) is an autosomal dominant cancer predisposition syndrome associated with an elevated risk for tumours of the breast, thyroid and skin. Lhermitte-Duclos disease (LDD) cosegregates with a subset of CD families and is associated with macrocephaly, ataxia and dysplastic cerebellar gangliocytomatosis. The common feature of these diseases is a predisposition to hamartomas, benign tumours containing differentiated but disorganized cells indigenous to the tissue of origin. Linkage analysis has determined that a single locus within chromosome 10q23 is likely to be responsible for both of these diseases. A candidate tumour suppressor gene (PTEN) within this region is mutated in sporadic brain, breast and prostate cancer. Another group has independently isolated the same gene, termed MMAC1, and also found somatic mutations throughout the gene in advanced sporadic cancers. Mutational analysis of PTEN in CD kindreds has identified germline mutations in four of five families. We found nonsense and missense mutations that are predicted to disrupt the protein tyrosine/dual-specificity phosphatase domain of this gene. Thus, PTEN appears to behave as a tumour suppressor gene in the germline. Our data also imply that PTEN may play a role in organizing the relationship of different cell types within an organ during development.

Killing and mutation of human lymphoblast cells by aflatoxin B1: evidence for an inducible repair response.

Diploid human lymphoblast cells exhibit apparent saturation of mutation induced by exposure to aflatoxin B1, despite a linear increase in the amount and proportion of the aflatoxin-DNA adducts formed. The saturation is neither a cell cycle phenomenon nor a result of a genetically heterozygous population. Examination of the biphasic nature of aflatoxin-DNA adduct loss in vivo shows initial, rapid removal of all adduct species, followed by a slow loss of the aflatoxin-N7-guanine adduct alone. We hypothesize that these data reveal two modes of adduct loss in these cells. The first is an inducible, error-free system that is short-lived, turning off as adduct levels fall below the induction threshold of some 1000 total adducts/cell. The second loss is slower and results from spontaneous depurination of remaining aflatoxin-N7-guanines. Our data are in agreement with the possibility that apurinic sites thus generated are responsible for the mutation observed. A major paradox arises from the fact that aflatoxin-related premutagenic depurinations are estimated to be only 10% of the number of spontaneous depurinations estimated by others to occur in human cells in a 1-h period.

Structural rearrangements of the WT1 gene in Wilms' tumour cells.

We have analysed 55 Wilms' tumour DNAs using the cDNA from the candidate Wilms' predisposition gene, WT1. One tumour, GOS 129, shows a partial homozygous deletion involving only the 3'-most exon of the gene. An adjacent 3' DNA sequence, J7-18, which lies on the same NotI fragment as WT1, is present in GOS 129. Thus, this partial deletion does not extend to the adjacent unmethylated 3' HTF island. These data support the candidature of WT1 as a Wilms' predisposition gene. Tumour GOS 129 has become homozygous as a result of a mitotic recombination event proximal to WT1. Three other tumours showed abnormally sized bands on Southern blot analysis which appear to reflect internal heterozygous rearrangements involving the 5' end of the gene. One of these tumours was from a bilaterally-affected patient and the other 3 were from stage III or IV tumours.

5-Azacytidine inhibits the induction of transient TK-deficient cells by 5-bromodeoxyuridine. A novel hypothesis for the facilitation of hypermethylation by 5-bromodeoxyuridine.

This paper examines the mechanism by which 5-bromodeoxyuridine (BrdUrd) induces a high frequency of transient trifluorothymidine (F3TdR)-resistant variants in the TK6 human lymphoblast cell line (a TK +/- heterozygote). This phenomenon has previously been termed 'pseudomutation' (Liber et al., 1985). We now report that 5-azacytidine (5-AzaC), an inhibitor of DNA methylation, reverses BrdUrd-induced pseudomutation in a dose-dependent manner. The inhibition by 5-AzaC is highly specific and does not appear to involve nucleotide pool perturbations. 5-AzaC inhibits the pseudomutagenic effect (transient trifluorothymidine resistance in a thymidine kinase heterozygote), but not the stable mutagenic effect (stable 6-thioguanine resistance or trifluorothymidine resistance in a hypoxanthine-guanine phosphoribosyltransferase-proficient cell) induced by BrdUrd. 5-AzaC did not affect the induction nor expression of mutation induced by several other chemical mutagens at either the tk or hgprt loci. Inhibition of pseudomutation by 5-AzaC did not appear to be caused by a number of potential confounding factors. Although significant changes in the levels of DNA methylation were detected by HPLC analysis in BrdUrd-treated cells, the dose response for inhibition of pseudomutation by 5-AzaC was correlated with a significant decrease in 5-methylcytidine levels. These results and additional data in the literature have led us to postulate a novel mechanism in which the substitution of BrdUrd in a TpG dinucleotide(s) may serve as a substrate for non-heritable methylation and hence transiently inactivate tk gene expression.

Cell-cycle dependent mutation of human lymphoblasts: bromodeoxyuridine and butyl methanesulfonate.

Cells of the human lymphoblast line WI-L2 and its derivative TK-6 were synchronized by centrifugal elutriation and cell-cycle dependent mutation to 6TGR (HPRT) and OUAR (Na+, K+ ATPase) measured. Bromodeoxyuridine induced 6TGR and OUAR mutations within S phase while butylmethyl-sulfonate induced mutation displayed no cell-cycle dependence. The data indicate that centrifugal elutriation is a facile means to obtain a useful degree of synchrony for these cell lines.

Molecular and biochemical analyses of spontaneous and X-ray-induced mutants in human lymphoblastoid cells.

We have isolated a series of 14 spontaneously arising and 28 X-ray-induced mutants at the hypoxanthine-guanine phosphoribosyltransferase (hgprt) locus in human lymphoblastoid cells. Among the spontaneous mutants, 5/14 (36%) had detectable alterations in their restriction fragment pattern after hybridization with a human cDNA probe for hgprt. Of the 10 remaining mutants, 4 had partial HGPRT enzyme activity, which suggested that they contained point mutations. Among the 28 mutants induced by 150 rad of X-rays, 15 (54%) had deletions of part or all of the hgprt gene. 5 of the remaining 13 (18% overall) had partial HGPRT enzyme activity, which suggested that they contained point mutations. These data imply that in this human cell system, X-rays induce both point mutants which have residual enzyme activity as well as mutations involving relatively large deletions of DNA.

Mutational and pseudomutational effects of 5-bromodeoxyuridine in human lymphoblasts.

We have studied the effects of 5-bromodeoxyuridine (BrdUrd) at two genetic loci in diploid human lymphoblast cells. In thymidine kinase heterozygotes (tk +/-), a 2-h dose of BrdUrd induced a transient, non-heritable resistance to the thymidine analogue, trifluorothymidine (F3TdR). We have called this phenomenon pseudomutation and have shown that affected cells acquire the ability to survive in the presence of F3TdR and then, after degradation of F3TdR in the medium, return to an apparently normal wild-type state. Our data suggest that BrdUrd incorporation into DNA as a thymidine analogue is responsible for the effect, which we interpret as a temporary loss of thymidine kinase activity. This effect is not seen in tk +/+ homozygotes. In contrast, at the hypoxanthine-guanine phosphoribosyl transferase locus in tk +/- heterozygotes, BrdUrd did not induce a permanent, heritable resistance to 6-thioguanine (gene locus mutation). We detected such mutations only in the tk +/+ homozygote and only at external BrdUrd concentrations considerably higher than those which saturate the uptake of BrdUrd into DNA as a thymidine analogue. We postulate that the reduced TK enzyme levels (30%) in the heterozygote prevent the build-up of a sufficiently high intracellular BrdUrd triphosphate pool to promote the misincorporations as deoxycytidine triphosphate which may be responsible for gene locus mutation.

Studies of mutagenicity and clastogenicity of 5-azacytidine in human lymphoblasts and Salmonella typhimurium.

5-Azacytidine (5-AzaC) induced mutation in the TK+/- human lymphoblastoid line, TK6, at both the thymidine kinase (tk) locus as measured by resistance to trifluorothymidine (F3TdR), and the hypoxanthine-guanine phosphoribosyltransferase (hgprt) locus, as measured by resistance to 6-thioguanine (6TG). F3TdRR and 6TGR mutant fractions induced by 5-AzaC were observed after a normal phenotypic expression time and remained stable. Interestingly, 5-AzaC was 5-10 times more mutagenic at the tk locus than the hgprt locus. However, F3TdRR colonies from 5-AzaC-treated cultures behaved like TK-deficient mutants induced by other chemical mutagens. The TK or HGPRT phenotype had no effect on the toxicity of 5-AzaC, thus eliminating differential toxicity as a potential cause for the observed higher mutability at the tk locus. 5-AzaC did not induce F3TdRR cells in the parental TK+/+ lymphoblastoid line, indicating that 5-AzaC-induced F3TdRR variants were not due to a dominant alteration in gene expression. 5-AzaC did not induce chromosomal aberrations in TK6 cells, eliminating clastogenic events as a potential cause for the higher mutability at the tk locus. 5-AzaC was also found to be mutagenic in a forward mutation assay to 8-azaguanine resistance in Salmonella typhimurium.

Cadmium-induced expression of immediate early genes in LLC-PK1 cells.

To identify molecular mechanisms underlying renal cell damage by cadmium, the effect of this heavy metal on the level of immediate early genes (IEGs) transcripts in LLC-PK1 cells was studied. Cadmium chloride (CdCl2) induced the expression of four IEGs examined, but with differing time courses. The level of c-fos mRNA peaked at 30 minutes, and then decreased. The levels of c-jun and c-myc transcripts reached a maximum at one hour, and remained elevated up to four hours. Egr-1 mRNA level peaked at one hour, and returned to the control level by three hours. Experiments with cycloheximide and actinomycin D showed, respectively, that induction of IEGs by cadmium occurred in a protein synthesis-independent and transcriptional activation-dependent manner. Cadmium induction of c-fos mRNA was reduced markedly by the intracellular calcium chelator, bis-(o-aminophenoxy)-ethane-N,N,N',N'-tetraacetic acid tetra(acetoxymethyl)-ester (BAPTA/AM), and was decreased partially by a protein kinase C (PKC) inhibitor, 1-(5-isoquinolinylsulfonyl)-2- methylpiperazine (H-7). These data indicate that IEG induction by cadmium requires intracellular calcium mobilization and occurs in part by a PKC-dependent pathway. Exposure of LLC-PK1 cells to CdCl2 (20 microM for 1 to 24 hr) resulted loss of cell viability and DNA fragmentation, which was indicative of apoptosis.

Wilms' tumor gene, WT1, mRNA is down-regulated during induction of erythroid and megakaryocytic differentiation of K562 cells.

Evidence implicates the product of the Wilms' tumor suppressor gene, WT1, in proliferation and differentiation of target tissues during development. Study of the regulation of other tumor suppressor genes during these processes has been instrumental in defining their interactions and functions. In this study, we performed experiments to assess the suitability of the human K562 erythroleukemia cell line for studying the WT1 gene during differentiation. We predicted that WT1 mRNA would be decreased during induction of differentiation of K562 cells based on observations of decreased WT1 mRNA during kidney development and in differentiated Wilms' tumors and leukemias. Accordingly, we found that WT1 mRNA was down-regulated in K562 cells during induction of erythroid and megakaryocytic differentiation by sodium butyrate and 12-O-tetradecanoylphorbol-13-acetate, respectively. Down-regulation of WT1 mRNA was not a generalized phenomenon of growth inhibition. WT1 mRNA was not down-regulated when 12-O-tetradecanoylphorbol-13-acetate-induced differentiation was blocked by bryostatin-1. During 12-O-tetradecanoylphorbol-13-acetate treatment, the decrease in WT1 mRNA was rapid (within 5 min), continuous, and occurred, at least in part, posttranscriptionally. An analysis of the 5' flanking region and transcription initiation sites of the human WT1 gene also was performed. Our data suggest that K562 cells will be a valuable system for unraveling signal transduction pathways by which WT1 is regulated and for investigating the interactions and role of WT1 in differentiation.

Alternative splicing and genomic structure of the Wilms tumor gene WT1.

The chromosome 11p13 Wilms tumor susceptibility gene WT1 appears to play a crucial role in regulating the proliferation and differentiation of nephroblasts and gonadal tissue. The WT1 gene consists of 10 exons, encoding a complex pattern of mRNA species: four distinct transcripts are expressed, reflecting the presence or absence of two alternative splices. Splice I consists of a separate exon, encoding 17 amino acids, which is inserted between the proline-rich amino terminus and the zinc finger domains. Splice II arises from the use of an alternative 5' splice junction and results in the insertion of 3 amino acids between zinc fingers 3 and 4. RNase protection analysis demonstrates that the most prevalent splice variant in both human and mouse is that which contains both alternative splices, whereas the least common is the transcript missing both splices. The relative distribution of splice variants is highly conserved between normal fetal kidney tissue and Wilms tumors that have intact WT1 transcripts. The ratio of these different WT1 mRNA species is also maintained as a function of development in the mouse kidney and in various mouse tissues expressing WT1. The conservation in structure and relative levels of each of the four WT1 mRNA species suggests that each encoded polypeptide makes a significant contribution to normal gene function. The control of cellular proliferation and differentiation exerted by the WT1 gene products may involve interactions between four polypeptides with distinct targets and functions.

Evidence for WT1 as a Wilms tumor (WT) gene: intragenic germinal deletion in bilateral WT.

The inactivation of two alleles at a locus on the short arm of chromosome 11 (band 11p13) has been suggested to be critical steps in the development of Wilms tumor (WT), a childhood kidney tumor. Two similar candidate WT cDNA clones (WT33 and LK15) have recently been identified on the basis of both their expression in fetal kidney and their location within the smallest region of overlap of somatic 11p13 deletions in some tumors. These homozygous deletions, however, are large and potentially affect more than one gene. Using a cDNA probe to the candidate gene, we have analyzed DNA from both normal and tumor tissue from WT patients, in an effort to detect rearrangements at this locus. We report here a patient with bilateral WT who is heterozygous for a small (less than 11 kb) germinal deletion within this candidate gene. DNA from both tumors is homozygous for this intragenic deletion allele, which, by RNA-PRC sequence analysis, is predicted to encode a protein truncated by 180 amino acids. These data support the identification of this locus as an 11p13 WT gene (WT1) and provide direct molecular data supporting the two-hit mutational model for WT.

An internal deletion within an 11p13 zinc finger gene contributes to the development of Wilms' tumor.

We have recently described the isolation of a candidate for the Wilms' tumor susceptibility gene mapping to band p13 of human chromosome 11. This gene, primarily expressed in fetal kidney, appears to encode a DNA binding protein. We now describe a sporadic, unilateral Wilms' tumor in which one allele of this gene contains a 25 bp deletion spanning an exon-intron junction and leading to aberrant mRNA splicing and loss of one of the four zinc finger consensus domains in the protein. The mutation is absent in the affected individual's germline, consistent with the somatic inactivation of a tumor suppressor gene. In addition to this intragenic deletion affecting one allele, loss of heterozygosity at loci along the entire chromosome 11 points to an earlier chromosomal nondisjunction and reduplication. We conclude that inactivation of this gene, which we call WT1, is part of a series of events leading to the development of Wilms' tumor.

Complete physical map of the WAGR region of 11p13 localizes a candidate Wilms' tumor gene.

A complete physical map of the 11p13 region containing the Wilms' tumor locus has been developed and used to localize a candidate Wilms' tumor gene. Our strategy to construct the map combined the use of pulsed-field gel electrophoresis and irradiation-reduced somatic cell hybrids. These hybrids, which contain limited segments of human chromosome 11 segregated from the remainder of the human genome, permit direct visualization of restriction fragments located in 11p13 using human interspersed repeated DNA sequences as hybridization probes. The physical map has provided a framework to identify the sites of genes responsible for the complex of disorders associated with hemizygous 11p13 deletion: Wilms' tumor, aniridia, genitourinary abnormalities, and mental retardation. The Wilms' tumor locus has been limited to a region of less than 345 kb, and a transcript with many of the characteristics expected for the Wilms' tumor gene has been localized to this region.

Mapping and characterization of 129 cosmids on human chromosome 11p.

We constructed cosmid libraries from human-hamster somatic cell hybrids that possess all or part of the short arm of chromosome 11 as their only human complement and isolated 129 human 11p clones. These cosmids map to 22 of 25 intervals distinguished by a hybrid panel for chromosome 11p. Forty-eight single-copy sequences were subcloned from 25 cosmids. Six of 17 (35%) single-copy sequences tested identify 11 new polymorphisms. Restriction endonuclease analysis identified CpG islands in 16 of 68 cosmids (23.5%). Analysis of the distribution of restriction endonuclease sites recognizing CpG dinucleotides showed that clusters of these sites, including those associated with the 5' region of an 11p13 Wilms' tumor gene, WT1, can span greater distances than generally recognized. The cosmids reported here should contribute to the construction of long-range physical maps and the isolation of additional genes on the short arm of chromosome 11.

Sequence analysis and functional characterization of the violacein biosynthetic pathway from Chromobacterium violaceum.

Violacein is a purple-colored, broad-spectrum antibacterial pigment that has a dimeric structure composed of 5-hydroxyindole, oxindole and 2-pyyrolidone subunits formed by the condensation of two modified tryptophan molecules. The violacein biosynthetic gene cluster from Chromobacterium violaceum was characterized by DNA sequencing, transposon mutagenesis, and chemical analysis of the pathway intermediates produced heterologously in Escherichia. coli. The violacein biosynthetic gene cluster spans eight kilobases and is comprised of the four genes, vioABCD, that are necessary for violacein production. Sequence analysis suggests that the products of vioA, vioC and vioD are nucleotide-dependent monooxygenases. Disruption of vioA or vioB completely abrogates the biosynthesis of violacein intermediates, while disruption of the vioC or vioD genes results in the production of violacein precursors.

Smallest region of overlap in Wilms tumor deletions uniquely implicates an 11p13 zinc finger gene as the disease locus.

The development of Wilms tumor (WT) has been associated with the inactivation of a "tumor suppressor" locus in human chromosome 11 band p13. Several WTs that exhibit homozygous deletions of an 11p13 candidate WT gene in its entirety have been reported. We report here a partial deletion of the candidate gene which, upon comparison with other documented homozygous deletions, permitted a precise definition of the critical genomic target in Wilms tumor. The smallest region of overlap between these deletions is a 16-kb segment of DNA encompassing the 5' exon(s) of an 11p13 gene coding for a zinc finger protein, together with an associated CpG island. This finding supports the notion that the candidate gene in question corresponds to the 11p13 WT1 Wilms tumor locus.

A genetic linkage map of 27 loci from PND to FY on the short arm of human chromosome I.

A genetic linkage map of 27 loci on the short arm of human chromosome 1 has been developed by analysis of the 40 families in the Centre d'Etude du Polymorphisme Humain (CEPH) reference panel. Probes that recognize 14 novel RFLPs at loci designated D1S9-D1S22 were isolated from a flow-sorted chromosome 1 library. A linkage map of chromosome 1p was constructed from the genotypic data at these 14 loci, RFLPs at eight cloned genes (PND, ALPL, FUCA1, SRC2, MYCL, GLUT, TSHB, and NGFB), two previously identified RFLPs (D1S2 and D1S57), two blood group antigens (RH and FY), and the isozyme PGM1. All 27 loci form a continuous linkage group, from FY to PND, of 102 cM in males and 230 cM in females. This map provides a basis for highly informative multipoint mapping studies for most of the short arm of chromosome 1.

Isolation and characterization of a zinc finger polypeptide gene at the human chromosome 11 Wilms' tumor locus.

We have isolated a series of genomic and cDNA clones mapping within the boundaries of constitutional and tumor deletions that define the Wilms' tumor locus on human chromosome 11 (band p13). The transcription unit corresponding to these clones spans approximately 50 kb and encodes an mRNA approximately 3 kb long. This mRNA is expressed in a limited range of cell types, predominantly in the kidney and a subset of hematopoietic cells. The polypeptide encoded by this locus has a number of features suggesting a potential role in transcriptional regulation. These include the presence of four zinc finger domains and a region rich in proline and glutamine. The amino acid sequence of the predicted polypeptide shows significant homology to two growth regulated mammalian polypeptides, EGR1 and EGR2. The genetic localization of this gene, its tissue-specific expression, and the function predicted from its sequence lead us to suggest that it represents the 11p13 Wilms' tumor gene.

Molecular studies of an ependymoma-associated constitutional t(1;22)(p22;q11.2).

We previously described a patient with a de novo constitutional translocation, t(1;22)(p22;q11.2), who developed a malignant ependymoma at age 5, and we proposed that the translocation predisposed the child to the development of the tumor. As a step toward isolation of a putative cancer gene, we have characterized the breakpoints of the (1;22) translocation at the molecular level. The chromosome 22 breakpoint has been narrowed to a region between ARVCF and D22S264. The chromosome 1 breakpoint has been mapped onto a doubly-linked Whitehead YAC contig by PCR analysis of the STS contents of the patient's derivative chromosomes isolated in somatic cell hybrids. Loss-of-heterozygosity (LOH) studies of the patient's ependymoma and of sporadic ependymomas showed no evidence of consistent loss in the breakpoint regions, suggesting that activation of an oncogene, rather than inactivation of a tumor suppressor gene, is the more likely molecular mechanism involved in this case. The gene for Edg-1, a neurally expressed, seven-segment transmembrane receptor, maps to the region of the chromosome 1 breakpoint but does not appear to be interrupted by the translocation. Molecular characterization of the breakpoint regions reported here represents an important step in the identification of the gene(s) affected by this translocation.