Huntington's disease: two families with differing clinical features show linkage to the G8 probe.

To test the hypothesis that interfamily variability in Huntington's Disease (HD) is due to mutation at different loci, linkage analysis was undertaken in two large HD kindreds that differed in ethnicity, age-at-onset, and neurologic and psychiatric features. Both families showed linkage of the HD locus to the G8 probe. Several recombinants were documented in each family, and the best estimate of the recombination fraction for the two families was 6 percent with a 95 percent confidence interval of 0 to 12 percent. Although the data support the existence of a single HD locus, use of the G8 probe for presymptomatic testing in these kindreds would have resulted in a 12 percent error rate in genotype assignment at the HD locus.

Nonrandom X chromosome DNA methylation patterns in hemophiliac females.

Molecular X chromosome inactivation analysis was used to characterize three females (and their families) with severe hemophilia. First, the maternal and paternal X chromosomes were distinguished by restriction fragment length polymorphisms (RFLPs). Second, the patterns of methylation of X chromosome genes using methylation-sensitive restriction endonucleases were determined. Of the six X chromosome probes tested, only the phosphoglycerol-kinase (PGK) and hypoxanthine-phosphoribosyl-transferase (HPRT) clones were informative, indicating that other X chromosome probes are not useful for X inactivation analysis. After digestion with Hpa II or Hha I, the hybridization intensity of the RFLPs of all three mothers and an unaffected sister were diminished by 50%, consistent with random X chromosome inactivation. The methylation patterns of the X chromosomes of the affected females, however, were clearly nonrandom. Depending upon the probe and the patient, HPRT and PGK sequences were either completely methylated or unmethylated. These findings are extremely suggestive that nonrandom X chromosome inactivation (lyonization) is the basis for severe hemophilia in these females.

Nonrandom distribution of N-myc oncogene genotypes in neuroblastoma.

The distributions of Pvu II and Sph I alleles of the N-myc oncogene (also known as MYCN) were studied in a series of normal individuals and pediatric patients with solid tumors. In the case of Pvu II, where the polymorphic site is located 3' of the gene, the frequencies of the allele were 0.27 (11-kilobase fragment) and 0.73 (8-kilobase fragment) in 43 unrelated normal Caucasians. The frequencies of the allele were similar in 40 non-N-myc-amplified neuroblastomas, 47 Wilms' tumors, and 31 other pediatric tumors. In these cases, the genotypes were in Hardy-Weinberg equilibrium. In 18 N-myc-amplified neuroblastomas, however, the observed genotype frequencies deviated from Hardy-Weinberg equilibrium (P less than .005). Similar observations were made with an Sph I restriction fragment length polymorphism where the polymorphic site is located in intron 2. The differences between amplified and nonamplified neuroblastomas suggest a possible involvement of sequences at or near N-myc in the progression of tumors where the N-myc gene is amplified.

N-myc oncogene RNA expression in neuroblastoma.

Tumor specimens from 33 patients with neuroblastoma were assayed for amplification of the N-myc oncogene and RNA expression to determine whether N-myc RNA expression levels correlated with N-myc gene amplification and clinical outcome. N-myc gene amplification was detected in one stage II tumor, one stage IV-S tumor, and seven stage III or IV tumors. In each case, N-myc RNA expression roughly paralleled N-myc gene amplification. However, enhanced N-myc RNA expression was not confined to tumors with N-myc gene amplification: all of the early (stage I and II) tumors, five stage IV-S tumors, and 12 advanced (stage III and IV) tumors had levels of N-myc RNA that were elevated up to 50-fold. While N-myc gene amplification correlated with prognosis, there was no such correlation with levels of N-myc RNA expression. The precise role of the N-myc gene in the pathogenesis of neuroblastoma remains unclear.

Allelic loss at chromosomes 3p, 8p, 13q, and 17p associated with poor prognosis in head and neck cancer.

BACKGROUND: Little is known about the molecular genetic events that contribute to the pathogenesis of squamous cell carcinoma of the upper aerodigestive tract. Previous molecular genetic studies have been limited to the identification of mutations of the p53 (also known as TP53) tumor suppressor gene, activation of a limited set of oncogenes, allelic loss at 3p and other locations, and occasional association with human papillomavirus infection. PURPOSE: Our purpose was to screen tumor tissue and blood from patients with squamous cell carcinoma of the upper aerodigestive tract for loss of heterozygosity at polymorphic loci corresponding to each of the autosomal chromosomes and to identify the locations of additional putative tumor suppressor genes, other than RB (also known as RB1) and p53, that may contribute to the pathogenesis of this disease. METHODS: Tumor tissue and blood were obtained from 68 consecutive patients with squamous cell carcinoma of the upper aerodigestive tract. In all cases, tumor tissue was obtained from the center of the surgical specimen. The relative absence of non-neoplastic tissue was confirmed by frozen-section histologic examination of immediately adjacent tissue. Initially, 30 paired tissue and blood samples were tested for loss of heterozygosity by polymerase chain reaction (PCR) to amplify 43 different highly polymorphic sequences containing small oligonucleotide repeats. After PCR amplification, with unique oligonucleotides flanking the repeat, visualization and sizing of the alleles on DNA sequencing gels were performed. Specific loss of heterozygosity was distinguished from random genetic loss due to generalized chromosomal instability if it occurred in more than 20% of specimens tested for a particular marker. RESULTS: Significant loss of heterozygosity (> 20%) occurred at alleles at chromosome bands 3p21 (32%), 3p25-26 (56%), 8pter-21.1 (31%), 13q14 (27%), and 17p12 (45%). Loss of heterozygosity at more than two loci was significant with a poor prognosis (P = .039). CONCLUSIONS: These findings demonstrate that squamous cell carcinoma of the upper aerodigestive tract exhibits genetic alterations at multiple loci and that allelic loss at more than two locations is indicative of a poor prognosis (the likelihood of the patient dying of disease). IMPLICATIONS: While tumor suppressor genes at 3p (VHL), 13q (RB), and 17p (p53) have been identified, altered genes at other loci on 3p and on 8p have not yet been characterized. Furthermore, the genotype at these loci for squamous cell carcinoma of the upper aerodigestive tract has prognostic importance and may identify the patients who should receive the most aggressive treatment.

Infrequency of MDM2 gene amplification in pediatric solid tumors and lack of association with p53 mutations in adult squamous cell carcinomas.

Loss of function of the p53 tumor suppressor gene by point mutation is the most commonly detected genetic alteration in human cancer. There is growing evidence that amplification and overexpression of the MDM2 gene are alternative mechanisms that also lead to functional inactivation of p53. While p53 mutations and MDM2 amplification have been reported to occur in rhabdomyosarcoma and osteogenic sarcoma, the incidence of MDM2 in other pediatric solid tumors is not known. We therefore tested a series of other pediatric solid tumors for MDM2 gene amplification. MDM2 amplification could not be detected in specimens from 40 Wilms' tumors, 15 neuroblastomas, 12 sarcomas, or 4 hepatoblastomas tested. To determine whether MDM2 amplification was an alternative mechanism of p53 inactivation in adult carcinomas that frequently possess p53 mutations, 68 samples of squamous cell carcinomas of the upper aerodigestive tract, 24% of which were previously shown to contain p53 mutations, were also tested for MDM2 amplification. MDM2 amplification did not occur in any of the tumor specimens tested. These findings suggest that MDM2 amplification may only occur in a limited subset of human tumors. Loss of function of p53 may be an essential event in human tumorigenesis. If so, then other mechanisms of p53 inactivation must occur in those tumors that exhibit neither p53 mutation nor MDM2 amplification.

Frequent allelic loss at chromosome arm 3p is distinct from genetic alterations of the Von-Hippel Lindau tumor suppressor gene in head and neck cancer.

Previous molecular genetic studies revealed that allelic loss of chromosome arm 3p is a frequent event in upper aerodigestive tract squamous cell carcinoma (UADT SCC). Recently, the Von-Hippel Lindau (VHL) tumor suppressor gene was identified at chromosome band 3p25-26. To determine if the VHL locus is altered in these tumors, a paired series of 26 tumors and blood from patients with UADT SCC that were previously shown to exhibit allelic loss of 3p were tested for LOH surrounding the VHL locus using four different polymorphic markers. All of the samples (100%) exhibited LOH for at least 1 marker. However, no LOH was detected using a polymorphism within exon 1 of the VHL gene which was informative for 18 of the 26 cases. Furthermore, mutations of the VHL gene could not be identified by single-strand conformation polymorphism, dideoxyfingerprint or direct DNA sequence analysis. In addition, the VHL gene was not inactivated by hypermethylation in any of the 26 tumor samples studied. These findings demonstrate that allelic loss of chromosome arm 3p in UADT SCC involves regions surrounding the VHL locus but does not include the VHL gene. The VHL gene, therefore, does not appear to be involved in the pathogenesis of UADT SCC.

Genetic alterations of chromosome band 9p21-22 in head and neck cancer are not restricted to p16INK4a.

Although genetic alterations of chromosome band 9p21-22 occur frequently in head and neck squamous cell carcinoma (HNSCC) cell lines, alterations of the cyclin-dependent kinase inhibitor p16INK4a located in this region are less common in corresponding primary tumors. To further investigate genetic alterations at 9p21-22 and p16INK4a in primary HNSCC, a paired set of 21 tumors and blood specimens that were shown previously to exhibit allelic loss at 3p and elsewhere, were tested for LOH at 9p21-22 using eight different highly polymorphic marker. Sixteen of the samples (81%) exhibited LOH for at least one marker. Frequent LOH was found surrounding p16INK4a and at three additional non-contiguous regions of 9p21-22. No homozygous deletions were identified. SSCP screening and direct sequence analysis led to the identification of mutations the p16INK4a gene in two tumors. p16INK4a was not hypermethylated in any of the samples studied. Furthermore, there was no correlation between LOH at 9p21-22 and the RB1 tumor suppressor gene. These findings indicate that in the set of tumors that we tested, LOH at 9p21-22 is common in primary HNSCC but that genetic alterations of p16INK4a located in this region are unusual. Additional tumor suppressor genes at 9p21-22 may therefore be involved in the pathogenesis of this tumor.

Infrequency of BRCA2 alterations in head and neck squamous cell carcinoma.

Alterations of BRCA2 result in increased susceptibility to breast cancer in both men and women (relative lifetime risks of 0.06 and 0.8 respectively). BRCA2 maps to 13q12-q13 and encodes a transcript of 10,157 bp. Other cancers that have been described in BRCA2 mutation carriers include those of the larynx. Human chromosome 13q has been shown previously by LOH studies to harbor several tumor suppressor genes for head and neck squamous cell carcinoma (HNSCCs). We therefore examined the role of BRCA2 in the development of these cancers. Only 6/22 (27%) of the laryngeal cancers we examined demonstrated LOH of the BRCA2-containing region. These and 10 other HNSCCs of different origins that were demonstrated by LOH studies to have lost the region of chromosome 13 containing BRCA2 were examined for alterations in this gene. SSCP analysis failed to reveal any alterations leading us to conclude that BRCA2 alterations are not frequently involved in the pathogenesis of HNSCCs and that the observed LOH of chromosome 13 loci is due to other, as yet, unidentified tumor suppressor gene(s). Interestingly tumors with LOH in this region (proximal to D13S118) were far more likely to be derived from women than men. This is unusual since HNSCCs are usually fourfold more common in men than in women.

Clonality of head and neck-carcinoma and adjacent mucosa.

Upper aerodigestive tract squamous cell carcinoma (UADT SCC) is associated with exposure to tobacco and ethanol and there is a high incidence of multifocal dysplasia, synchronous/metachronous lesions and local recurrence. These observations led to a 'field cancerization' hypothesis which proposes that the entire expanse of carcinogen-exposed mucosa is predisposed to neoplasia. This hypothesis implies that UADT SCC arises from multiple sites and is therefore polyclonal. To test this hypothesis, eight paired tumor and blood samples and 4 specimens of adjacent normal mucosa were tested for clonality by molecular X chromosome inactivation analysis. While tumor specimens were clonal, normal mucosa and blood were polyclonal. These findings demonstrate that UADT SCC is a clonal neoplasm that arises from polyclonal mucosa and supports an alternative interpretation of the 'field cancerization' theory which states that multiple sites are at risk and each neoplasm arising from these different sites is monoclonal.

p53, retinoblastoma, and human papillomavirus in squamous cell carcinoma and adjacent normal mucosa of the upper aerodigestive tract.

OBJECTIVE: The primary objective of this study was to determine the incidence of p53 and retinoblastoma tumor suppressor gene mutations and human papillomavirus infection in squamous cell carcinoma and adjacent normal mucosa of the upper aerodigestive tract. The secondary objective was to associate these findings with clinical and histopathologic features. DESIGN: Point mutations of p53 were identified by single-strand conformation polymorphism analysis and confirmed by direct DNA sequence analysis. Polymerase chain reaction-based methods were used to identify loss of heterozygosity of the retinoblastoma tumor suppressor gene and the presence of human papillomavirus sequences. SETTING: University-based tertiary care center. PATIENTS OR OTHER PARTICIPANTS: Forty-five consecutive cases of upper aerodigestive tract squamous cell carcinoma. RESULTS: Eleven point mutations of p53 were identified in tumor samples (24%). No functional p53 mutations were detected in adjacent normal tissue from eight of these individuals nor was there evidence of p53 alteration in normal tissue adjacent to 12 of 30 additional tumors tested that demonstrated conformational alterations by single-strand conformation polymorphism analysis. The p53 mutations were significantly associated with local invasion. Loss of heterozygosity (which has a 20% chance of random occurrence in tumors) was detected at the retinoblastoma locus in 15% of the tumors tested. Five of the specimens (11%) were positive for human papillomavirus sequences (two of which also contained p53 mutations). CONCLUSIONS: These findings suggest that p53 but not retinoblastoma or human papillomavirus is an important prognostic factor and is involved as a late event in the pathogenesis of upper aerodigestive tract squamous cell carcinoma.

Infrequency of ras, p53, WT1, or RB gene alterations in Wilms tumors.

BACKGROUND: Alteration of the ras family of oncogenes and of the tumor suppressor genes p53 and RB are the most common genetic events in human tumors. Although there have been no reports of the prevalence of these alterations in Wilms tumors, overexpression of the N-myc and insulin-like growth factor-II (IGF-II) genes have been observed, and alteration of another tumor suppressor gene (WT1) has been demonstrated. METHODS: Forty-four Wilms tumor specimens were tested for the presence of N-, K-, and H-ras mutations in codons 12, 13, and 61 by single-strand conformation polymorphism (SSCP) analysis and direct DNA sequence analysis. Sixteen tumors were tested for abnormalities of WT1 by Southern and northern blot analysis and reverse transcriptase polymerase chain reaction (RT-PCR). N-myc, c-myc, WT1, and IGF-II mRNA expression was measured in 16 tumors by Northern blot analysis. Thirty-eight tumors were screened for p53 mutations by SSCP analysis and direct DNA sequence analysis. Nine tumors were analyzed for loss of heterozygosity (LOH) of RB. RESULTS: Although the authors confirmed that N-myc and IGF-II are overexpressed in Wilms tumors, no mutations of ras family, p53, or RB genes were identified, and no gross alterations of WT1 were detected by Southern or Northern blot analysis. CONCLUSIONS: These findings suggest that H-ras, K-ras, N-ras, p53, and RB are not involved in the pathogenesis of Wilms tumor.

The spectrum of beta-thalassemia genes in China and Southeast Asia.

To make possible prenatal diagnosis of beta-thalassemia in China and Southeast Asia by direct detection of mutant beta-globin genes, we have determined the spectrum of mutations producing the disorder in this region of the world. Seventy-eight beta-thalassemia genes from Chinese and Southeast Asians were randomly obtained, and the relevant mutation was characterized in 76 (98%) of them. Seven different point mutations were found among the 78 genes studied. Of these seven beta-thalassemia alleles, two constitute 62%, and two others account for 29% of the total. Since only four alleles make up 91% of the mutant genes, prenatal diagnosis of beta-thalassemia in China and Southeast Asia should be feasible by simplified techniques for direct detection of point mutations.

Use of haplotype analysis in the beta-globin gene cluster to discover beta-thalassemia mutations.

DNA polymorphisms have been of great value in defining a small number of common sequences in the beta-globin gene cluster and a region within which recombination may be restricted. Moreover, they have led to a screening procedure that not only has been of great value for the molecular characterization of beta-thalassemia mutations but also has implications for the characterization of other single-gene disorders.

Molecular phenotype of a pediatric small round cell tumor.

Molecular probes were used to characterize an unusual small round cell abdominal tumor arising from the fallopian tube of a 15-year-old girl. DNA and RNA extracted from the tumor and adjacent normal tissue was subjected to Southern and Northern blot analysis using a variety of different probes. N-myc oncogene RNA was greatly expressed in the tumor, but was not expressed in normal tissue or amplified in chromosomal DNA. Insulin-like growth factor II RNA was similarly overexpressed in the neoplasm, but not in normal tissue. While histopathologic studies could not distinguish between a neuroectodermal neoplasm and Wilms' tumor, electron microscopy and the pattern of gene expression was most consistent with Wilms' tumor.

Chinese A gamma fetal hemoglobin: C to T substitution at position-196 of the A gamma gene promoter.

The molecular basis for the hereditary persistence of fetal hemoglobin (HPFH) phenotype was studied in a Chinese individual who was heterozygous for a nondeletion form of A gamma-HPFH. Both allelic A gamma-globin genes were isolated by molecular cloning and subjected to nucleotide sequence analysis. One A gamma gene promoter showed a cytosine to thymine transition at position -196, whereas the other promoter was normal. This mutation at position -196 has now ben found in unrelated individuals with the A gamma-HPFH phenotype from Italy, Sardinia, and China, suggesting that it may have arisen independently. The implications of this mutation for models of fetal globin gene switching are discussed.

p53 mutations, O6-alkylguanine DNA alkyltransferase activity, and sensitivity to procarbazine in human brain tumors.

BACKGROUND: In human brain tumors, sensitivity to procarbazine as measured by sensitivity in a xenograft tumor model correlated inversely with amounts of the DNA repair enzyme O6-alkylguanine DNA alkyltransferase (AT). METHODS: To test the hypothesis that mutations of the p53 tumor suppressor gene in human tumors also can correlate with the response to chemotherapy, p53 mutations2 were identified in primary human malignant brain tumors and cell lines in which AT activity and procarbazine sensitivity in a xenograft model was ascertained. RESULTS: Mutations were identified in 7 of 21 (33%) specimens tested. Specimens containing p53 mutations tended to exhibit an increased growth delay in procarbazine-treated xenografts and lower amounts of AT. CONCLUSIONS: p53 mutations in brain tumors may contribute to procarbazine sensitivity by failing to induce arrest at the G1/S cell-cycle checkpoint, thereby preventing the repair of procarbazine-induced genetic alterations.

N-myc oncogene expression in porcine renal development and oncogenesis.

N-myc oncogene expression was characterized in porcine kidneys to investigate the potential role of this gene in normal renal development and oncogenesis. N-myc RNA expression was detected in porcine kidneys from birth until 5 wk of age, which corresponds to the time when glomerular differentiation is completed. Immunohistochemical studies revealed that N-myc protein was selectively expressed in the primordia of renal proximal tubule epithelial cells. These cells were cultured in vitro and continued to express N-myc for a limited time. Comicroinjection of a mutant ras oncogene and N-myc into these cells led to focus formation in soft agar, loss of contact inhibition, and the establishment of an immortalized cell line. These findings support a multistep model of renal oncogenesis that involves overexpression of N-myc.

Use of oligonucleotide hybridization in the characterization of a beta zero-thalassemia gene (beta 37 TGG----TGA) in a Saudi Arabian family.

Analysis of restriction site polymorphisms in the beta-globin gene cluster of a Saudi Arabian female with beta zero-thalassemia demonstrated that both of her beta-globin genes were missing a nonpolymorphic AvaII site in exon 2. Examination of the normal nucleotide sequence surrounding this AvaII site revealed that either of two nucleotide substitutions, TGG----TAG or TGG----TGA, could produce a nonsense codon at codon 37 and eliminate the AvaII site. Consequently, two oligonucleotides (19-mers spanning codons 36 through 41 and containing either TAG or TGA at codon 37) were synthesized and hybridized against genomic DNA of the proband and her family. Specific hybridization with one of the oligomers demonstrated that the patient's beta o-thalassemia was the result of homozygosity for the TGG----TGA mutation at codon 37. In certain cases, oligonucleotide hybridization using genomic DNA may obviate the need for gene cloning and sequencing in the characterization of point mutations.