Genetic changes in the RNA components of RNase MRP and RNase P in Schmid metaphyseal chondrodysplasia.

BACKGROUND: The Schmid type of metaphyseal chondrodysplasia (MCDS) is generally due to mutations in COL10A1 encoding for type X collagen of cartilage. METHODS: We performed a study on the genes coding for the RNA components of RNase MRP (MRPR) and RNase P (H1RNA) among 20 patients with diagnosis of MCDS and no mutations in COL10A1. RESULTS: Two patients were found to be homozygous for a base substitution G for A at nucleotide 70 of RMRP, which is the major mutation causing cartilage-hair hypoplasia. No pathogenic mutations were detected in H1RNA. CONCLUSION: Cartilage-hair hypoplasia diagnosis should be considered in patients with metaphyseal chondrodysplasia even in the absence of any extra-skeletal manifestations if no mutation in COL10A1 can be found and the family history is compatible with autosomal recessive inheritance. Correct diagnosis is important for genetic counselling and for proper follow up of the patients.

Dynamic expression and nuclear accumulation of beta-catenin during the development of hair follicle-derived structures.

Beta-catenin has a dual role in the cell. At the membrane, it connects E-cadherin to the actin cytoskeleton, while in the nucleus, it controls gene expression in concert with Tcf-like transcription factors. Nuclear translocation of beta-catenin is induced by the Wnt signal transduction pathway. Control of this process is essential since elevated beta-catenin levels interfere with differentiation and development, and can initiate cancer in many tissues. An important role for beta-catenin during hair follicle related development and tumorigenesis has recently been established, though little is known of its endogenous expression during the development of these structures. Here, we have investigated the expression of beta-catenin in relation to markers for proliferation, differentiation and Wnt signaling during the development of three hair follicle related structures, i.e. whiskers, normal body hair and the preputial gland, and a hair follicle-derived tumor, the epidermal cyst. We observed nuclear accumulation of beta-catenin, the hallmark of Wnt signaling, in the upper matrix, the dermal papilla, the developing ringwulst of the whisker and in the tumor, though it was never in association with proliferation or terminal differentiation. Co-localization of nuclear beta-catenin with Tcf-3/4 was found only in the dermal papilla and the developing ringwulst of the whisker, but not in the upper matrix or in the tumor. These results further elucidate the role of the Wnt signal transduction pathway during hair follicle related development and tumorigenesis and illustrate the dynamic role of beta-catenin in signal transduction and cell-adhesion.

Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, cartilage-hair hypoplasia.

The recessively inherited developmental disorder, cartilage-hair hypoplasia (CHH) is highly pleiotropic with manifestations including short stature, defective cellular immunity, and predisposition to several cancers. The endoribonuclease RNase MRP consists of an RNA molecule bound to several proteins. It has at least two functions, namely, cleavage of RNA in mitochondrial DNA synthesis and nucleolar cleaving of pre-rRNA. We describe numerous mutations in the untranslated RMRP gene that cosegregate with the CHH phenotype. Insertion mutations immediately upstream of the coding sequence silence transcription while mutations in the transcribed region do not. The association of protein subunits with RNA appears unaltered. We conclude that mutations in RMRP cause CHH by disrupting a function of RNase MRP RNA that affects multiple organ systems.

Integrated high-resolution BAC, P1, and transcript map of the CHH region in chromosome 9p13.

A bacterial artificial chromosome (BAC) and P1 contig of the proximal part of chromosome 9p centromeric of markers D9S165 and D9S304 is described. This 1.1- to 1.7-Mb portion of chromosome 9p13 was previously not physically mapped. It contains 24 genes or expressed sequence tags, five polymorphic AC repeats, and three new polymorphic single-strand conformation polymorphism variants. Several of the genes thus mapped are excellent candidates for disease-causing genes whose loci have previously been assigned to proximal 9p. Our primary interest is in the cartilage-hair hypoplasia gene (CHH) that resides within the contig between markers D9S163 and D9S1791 based on linkage evidence.

Chromosomal localization of the human diadenosine 5',5"'-P1,P4-tetraphosphate pyrophosphohydrolase (Ap4A hydrolase) gene (APAH1) to 9p13.

Diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A) hydrolase is the enzyme responsible for maintaining the intracellular level of the dinucleotide Ap4A, the function of which has yet to be established. The APAH1 gene encoding this Ap4A hydrolase has been mapped by fluorescence in situ hybridization and PCR to human chromosome 9p13. Radiation hybrid panel mapping further located APAH1 between the IL11RA and the GALT genes, thus excluding it as a candidate gene for cartilage-hair hypoplasia, which maps proximal to GALT. Several tumor suppressor genes have previously been mapped within the 9p13-p21 region. Given that the FHIT gene at 3p14.2, which encodes a diadenosine 5',5"'-P1,P3-triphosphate (AP3A) hydrolase, is a candidate tumor suppressor, APAH1 should also be considered a potential tumor suppressor.

A serine/threonine kinase gene defective in Peutz-Jeghers syndrome.

Studies of hereditary cancer syndromes have contributed greatly to our understanding of molecular events involved in tumorigenesis. Here we investigate the molecular background of the Peutz-Jeghers syndrome (PJS), a rare hereditary disease in which there is predisposition to benign and malignant tumours of many organ systems. A locus for this condition was recently assigned to chromosome 19p. We have identified truncating germline mutations in a gene residing on chromosome 19p in multiple individuals affected by PJS. This previously identified but unmapped gene, LKB1, has strong homology to a cytoplasmic Xenopus serine/threonine protein kinase XEEK1, and weaker similarity to many other protein kinases. Peutz-Jeghers syndrome is therefore the first cancer-susceptibility syndrome to be identified that is due to inactivating mutations in a protein kinase.

Spectrum of spontaneous and 2,4,6-trinitrotoluene (TNT)-induced mutations in Salmonella typhimurium strains with different nitroreductase and O-acetyltransferase activities.

Spontaneous and 2,4,6-trinitrotoluene (TNT)-induced mutation spectra were determined at the hisD3052 allele of Salmonella typhimurium strains TA98, YG1021 (nitroreductase-overproducing) and YG1024 (O-acetyltransferase-overproducing). In TA98, 55% (11/20) of the spontaneous reversions and 95% (19/20) of reversions in TNT-treated plates were deletions of two bases at the same site (-2 hotspot deletions), whereas the respective figures were 65% (13/20) and 80% (16/20) in YG1021, and 75% (15/20) and 95% (19/20) in YG1024. Other mutations observed in the TNT treatment were complex frameshifts consisting of either a -2 hotspot deletion and a base substitution, or a +1 addition and base substitution at the stop codon. In addition, different kinds of deletions were recovered in the spontaneous spectra. The elevated enzymatic activities of strains, YG1021 and YG1024, resulting in enhanced mutagenicity of TNT, did not seem to have an effect on the spectrum of TNT-induced mutations. However, the YG strains, which also have a higher spontaneous revertant yield than the parental strain TA98, seemed to differ from TA98 in their spontaneous spectra. The increase consisted of revertants containing the -2 hotspot deletion, possibly indicating elevated activation of exogenous or endogenous premutagens by the higher enzyme activities of the YG strains.

Molecular cloning of a novel human CC chemokine secondary lymphoid-tissue chemokine that is a potent chemoattractant for lymphocytes and mapped to chromosome 9p13.

By searching the Expressed Sequence Tag (EST) data base, we identified partial cDNA sequences potentially encoding a novel human CC chemokine. We determined the entire cDNA sequence which encodes a highly basic polypeptide of 134 amino acids total with a putative signal peptide of 23 amino acids. The predicted mature protein of 111 amino acids has the four canonical cysteine residues and shows 21-33% identity to other human CC chemokines, but has a unique carboxyl-terminal extension of about 30 amino acids which contains two extra cysteine residues. The mRNA was expressed strongly in tissues such as the lymph nodes, Appendix, and spleen. The recombinant protein, which was produced by the baculovirus system and purified to homogeneity, was a highly efficient chemoattractant for certain human T cell lines and a highly potent one for freshly isolated peripheral blood lymphocytes and cultured normal T cells expanded by phytohemagglutinin and interleukin 2. Unlike most other CC chemokines, however, this novel chemokine was not chemotactic for monocytes or neutrophils, suggesting that it is specific for lymphocytes. From these results, we designated this novel CC chemokine as SLC from secondary lymphoid-tissue chemokine. SLC fused with the secreted form of alkaline phosphatase (SLC-SEAP) was used to characterize the SLC receptor. Binding of SLC-SEAP to freshly isolated lymphocytes was blocked by SLC (IC50, 0.12 nM) but not by any other CC chemokine so far tested, suggesting that resting lymphocytes express a class of receptors highly specific for SLC. By using somatic cell hybrids, radiation hybrids, and selected yeast and bacterial artificial chromosome clones, we mapped the SLC gene (SCYA21) at chromosome 9p13 and between chromosomal markers, D9S1978(WI-8765) and AFM326vd1, where the gene for another novel CC chemokine termed ELC from EBI1-ligand chemokine (SCYA19) also exists. Collectively, SLC is a novel CC chemokine specific for lymphocytes and, together with ELC, constitutes a new group of chemokines localized at chromosome 9p13.

Refined localisation of the genes for nebulin and titin on chromosome 2q allows the assignment of nebulin as a candidate gene for autosomal recessive nemaline myopathy.

A locus for autosomal recessive nemaline myopathy (NEM2) has been assigned by linkage analysis to a 13-cM region between the markers D2S150 and D2S142 on 2q21.2-q22. The genes for the giant muscle proteins nebulin and titin have previously been assigned by FISH to 2q24.1-q24.2 and 2q31, respectively. By using radiation hybrid mapping, we have reassigned the nebulin gene close to the microsatellite marker D2S2236 on 2q22 and the titin gene to the vicinity of the markers D2S384 and D2S364 on 2q24.3. The genomic orientation of the nebulin gene was determined as 5'-3' and of TTN as 3'-5' from the centromere. We conclude that the nebulin gene resides within the candidate region for NEM2 on the long arm of chromosome 2, while the titin gene is located outside this region.

Uniparental disomy in cartilage-hair hypoplasia.

Cartilage-hair hypoplasia (CHH) is an autosomal recessive disorder that presents with pleiotropic manifestations including impaired skeletal growth and cellular immunity. It is most prevalent among two founder populations, the Old Order Amish in the USA and the Finns. The gene has been localized to 9p13 by linkage analysis and linkage disequilibrium mapping. A statistically significant deficiency of affected members resulting in a lower than expected segregation ratio has been reported in the Amish, but was not found in a previous study in Finnish CHH families. Reduced penetrance was the mechanism suggested in the Amish, but could not be verified by haplotype analyses performed after the assignment of the CHH gene. Here we have carried out segregation analysis of 101 Finnish CHH families, but again, evidence of a significant deficiency of affected members was not found. Nevertheless, among 54 uniplex families, 2 patients with CHH and uniparental disomy (UPD) for chromosome 9 were discovered. UPD might contribute to low segregation ratios by increasing the number of families with only 1 affected individual. These observations show that UPD may occur in an unexpectedly high number of the patients and should be taken into account in the genetic counselling and prenatal diagnostics of CHH families.

A molecular and epidemiological study on bladder cancer: p53 mutations, tobacco smoking, and occupational exposure to asbestos.

In this study, we found an unexpected association (crude odds ratio = 2.8; 95% confidence interval = 0.9-8.4) between definite work-related exposure to asbestos and carcinoma of the urinary bladder in a small group of patients (n = 28) initially recruited as referents for an epidemiological feasibility study on the occupational causes of lung cancer. We extended the study by using molecular methods to examine mutations in the p53 tumor suppressor gene in the same cases of bladder cancers. The same number of archival samples of transitional cell carcinoma, mainly of grade 3, were added to the analysis. We failed to show any association between occupational exposure to asbestos and p53 mutations among bladder cancer patients. We observed an increasing occurrence of p53 mutations in nonsmokers (5 of 17, 29%), former smokers (8 of 21, 38%), and current smokers (9 of 16, 56%) in that order; however, this was not statistically significant. The most prevalent type of mutation was G:C to A:T transition. Tumor grade was not associated with the frequency of mutations, but the higher stage (T3-T4) tumors appeared to have mutations more frequently than did the less invasive tumors (T1-T2).

p53 antibodies in the sera of lung cancer patients: comparison with p53 mutation in the tumour tissue.

This study examined the sensitivity and specificity of serum auto-antibodies to p53 protein as a non-invasive marker of p53 genetic alterations or protein accumulation in lung cancer cases. A sensitive ELISA to detect serum p53 antibodies was developed and used to examine sera from 186 patients undergoing pulmonary surgery for a suspected lung cancer. Target antigens in ELISA were wild-type p53 protein and 5 peptides covering the N- and C-terminal parts of the protein. Sixteen sera were positive for serum p53 antibodies in both ELISAs and all were among the 136 patients with confirmed primary lung carcinoma. Of 50 patients with other pulmonary diseases, none had p53 antibodies. In 92 cancer patients exons 5 to 8 of the p53 gene were examined for mutations by denaturing gradient gel electrophoresis and direct sequencing of PCR products. Forty-seven tumours had a p53 mutation and 7 (15.2%) of these were positive for p53 antibodies. Two patients had serum antibodies but no detectable mutation in exons 5 to 8. Frequencies of p53 mutations and serum antibodies were higher in squamous cell carcinoma patients than in adenocarcinoma. Accumulation of p53 protein in tumour tissue was observed in 32 patients, but only 5 were positive for p53 antibodies. In conclusion, serum p53 antibodies were detected only in a proportion of lung cancer cases, but the majority were specifically associated with a detectable p53 mutation in the tumour.

Detection of loss of heterozygosity in the p53 tumor suppressor gene using a PCR-based assay.

Inactivation of the p53 tumor suppressor gene has been reported to be a prognostic factor in several human cancer types. Normal function of the gene is affected by deletion in one allele; dysfunction of the other allele is often caused by a mutation. In tumors of heterozygous individuals, deletion of one allele can be detected as loss of heterozygosity (LOH). A recently found variable number of tandem repeats (VNTR) segment in intron 1 of the p53 gene seems to be highly polymorphic and, therefore, a very useful marker in detecting LOH in various types of tumor samples. We in vitro amplified the VNTR segment from genomic DNA samples of 101 lung cancer patients and run conventional agarose gel electrophoreses in order to detect the alleles of various length, differing by the number of repeats. The usefulness of the method was studied using DNA from white blood cell samples and from fresh and formalin-fixed, paraffin-embedded tumor samples. Of the patients, 56% were found to have two different alleles, i.e. were informative in this assay. In 18% of the lung tumors from the informative cases, LOH in the p53 suppressor gene was detected.

Comparison of DGGE and CDGE in detection of single base changes in the hamster hprt and human N-ras genes.

Denaturing gradient gel electrophoresis (DGGE) and constant denaturant gel electrophoresis (CDGE) are methods based on sequence-determined melting characteristics of DNA and thus detect different types of single base changes in the amplified fragments. We have studied detection of 19 mutations in the human N-ras oncogene and 10 mutations in exon 3 of the Chinese hamster hypoxanthine-guanine phosphoribosyltransferase (hprt) gene using GC-clamped DGGE and CDGE. After allowing formation of heteroduplexes with the corresponding wild type sequence, all the mutations separated from the wild type in at least one concentration of the denaturants used in CDGE but two of the mutations in hprt exon 3 did not show separation in any of the DGGE runs. Melting behavior of the mutant fragments was dependent, as expected, on both the type and the location of a mutation. We describe conditions allowing separation of the mutations in the fewest possible DGGE and CDGE runs.

p53 and ras gene mutations in lung cancer: implications for smoking and occupational exposures.

This paper reviews mutational activation of ras oncogenes and inactivation of the p53 tumor suppressor gene in human lung cancer. We discuss the frequency, type, and location of mutations in these genes in relation to known etiological factors for lung cancer. The most studied examples of these are exposure to tobacco smoke, and to radon and asbestos fibers at work. We summarize data from our laboratory on K-ras and p53 mutations in fresh tissue samples from patients with resected primary lung carcinoma whose smoking and occupational histories were known. Most of the tumors examined were histologically non-small cell carcinoma (NSCLC), mainly of the squamous cell carcinoma and adenocarcinoma types. We compare the prevalence and nature of mutations in the two histological types of NSCLC.

Detection of serum p53 protein in lung cancer patients.

Serum levels of p53 protein were examined in 23 cases of lung cancer (many with potential asbestos exposure), 23 unexposed matched hospital control subjects, 58 unmatched general population control subjects, and 4 people with nonmalignant lung disease using an enzyme-linked immunosorbent assay and Western immunoblotting. Average levels of serum p53 in the lung cancer patients (0.55 ng/mL) were higher than in the cases of nonmalignant lung disease (0.42 ng/mL) or in the matched (0.32 ng/mL) or unmatched (0.31 ng/mL) control subjects, but the differences were not statistically significant. However, three of the cases of lung cancer (13%) were found to have serum p53 levels much greater than those of the control subjects (> 2 SD above the mean) and to have confirmatory positive Western blots for p53. The tumors from these subjects demonstrated increased levels of p53 in the tissue by immunohistochemistry and/or the presence of mutations in the p53 gene. These results suggest that p53 protein can be detected in serum in a portion of lung cancer cases with p53 alterations in the tumor tissue.

Genetic alterations in p53 and k-ras in lung-cancer in relation to histopathology of the tumor and smoking history of the patient.

The inactivation of the p53 suppressor gene and the activation of the ras proto-oncogenes are frequent events in non-small cell lung cancer as well as in many other solid neoplasms in man. Somatic mutations in exons 5-8 of the p53 gene were detected in 59% (30/51) of the squamous cell carcinoma and in 38% (14/37) of the adenocarcinoma tumors using GC-clamped, non-radioactive denaturing gradient gel electrophoresis (DGGE). The mutations in the exons 5 and 8 represented larger proportion of the alterations in squamous cell carcinoma tumors (p=0.04; Fisher's exact test, two-tailed); in the adenocarcinoma tumors, mutations were most common in the exon 7 of p53. Most of the identified mutations (25/39; 64%) are predicted to cause an amino acid substitution. Mutations leading to the premature termination of translation were more frequent in adenocarcinoma (6/14) than in squamous cell carcinoma (3/30) tumors (p=0.02). In adenocarcinoma, also base substitutions in the K-ras gene were detected more often (18/37; 49%) than in squamous cell carcinoma (p<0.01). However, a mutation both in p53 and Kras was detected in only 4% of the lung tumors which does not support importance of co-operation between the genes in vivo. Mutations in p53 and K-ras did not correlate with tumor differentiation in either histological type. In squamous cell carcinoma, mutations in p53 showed relation to pack years smoked whereas in adenocarcinoma, mutations in the K-ras gene were associated with cigarette consumption. G to T transversion was the most common type of base substitution in both genes (31% in p53 and 53% in K-ras).

K-ras oncogene codon 12 point mutations in testicular cancer.

A significant association between N-ras oncogene activating point mutations and testicular cancer has recently been reported. We have studied DNA samples from the blood and fresh tumor tissues of 17 Norwegian testicular cancer patients (11 seminomas/6 nonseminomas). Point mutations in K-ras-2 and N-ras exons 1 and 2 were studied by denaturing gradient gel electrophoresis (DGGE) and by oligonucleotide hybridization. No N-ras mutations were detected in these tumor samples, but two K-ras-2 exon 1 mutations were found in two of the seminoma tumors (stage I and II tumors) using the DGGE technique. The mutations were confirmed by dot blotting and oligonucleotide hybridization and identified as a G-->T and a G-->A point mutation in K-ras-2 codon 12, leading to a valine and a serine substitution, respectively. All the white blood cell DNAs were negative. As a positive control for DGGE screening, we ran two plasmid constructs carrying human N-ras exon 2 sequences with mutations. To study the role of ras gene activation in testicular cancer, a larger tumor sample population will be investigated.

Denaturing gradient gel electrophoresis (DGGE) assay for K-ras and N-ras genes: detection of K-ras point mutations in human lung tumour DNA.

Point mutations in the ras oncogenes are very common in lung cancers as well as in many of the other solid tumours. To effectively examine the occurrence of these mutations in a large number of tumour samples, we have applied denaturing gradient gel electrophoresis (DGGE) for the analysis of point mutations of the K-ras and N-ras genes, using GC-clamped, PCR-amplified DNA fragments. Among the 68 tumour DNA samples, we detected 14 mutations in the K-ras gene. This was 78% of the mutations identified by oligonucleotide hybridization. Altogether, eight of the nine different kinds of base substitutions found in the tumour samples were detected by the DGGE assay, representing substitutions at codons 12, 13, and 61 of the K-ras gene. Six of the detected mutations were guanine to thymine transversions at codon 12; this was the most common type of alteration. On the basis of our experience, the present non-radioactive DGGE analysis seems to be readily applicable for detection of the mutations in the K-ras and N-ras genes. Types of ras gene mutations frequent in adenocarcinomas of the lung are also discussed.