A mapped set of DNA markers for human chromosome 17

A prospective study of the significance of gene and chromosome alterations as prognostic indicators of breast cancer patients with lymph node metastases

In 150 surgically resected primary breast carcinomas that had axillary lymph-node metastases, we examined the incidence of loss of heterozygosity on chromosomes 16p, 16q, 17p, 17q, and 18q, point mutation of the p53 tumor-suppressor gene, nuclear immunoreaction of p53 protein, and amplifications of the c-erbB-2 and int-2 oncogenes by Southern blotting, single-strand conformation polymorphism analysis, and immunohistochemistry. We analyzed the association of these factors and conventional prognostic parameters with outcome of the patients, using Cox's univariate and multivariate analyses. The univariate analysis revealed that nuclear p53 immunoreaction, p53 mutation, and c-erbB-2 amplification as well as the number of metastatic lymph nodes, histological grade, and hormone-receptor statuses were significant prognostic indicators for both recurrence and cancer death. p53 immunoreaction was correlated more strongly with a poor prognosis than p53 mutations. The combination of p53 and c-erbB-2 effectively identified the high-risk patient group, and even among Grade 3 cases the subgroup with these alterations tended to have poorer clinical outcomes. The multivariate analysis including p53, c-erbB-2, and conventional factors. Lymph node status, grade, and p53 had independent impacts on the survival of patients. Under identical adjuvant systemic therapies, prognoses differed between the patient groups with and without alterations of p53 or c-erbB-2. Appropriate combinations of conventional factors with nuclear p53 immunoreaction and c-erbB-2 amplification would help to identify highly aggressive node-positive breast carcinomas and would aid stratification of patient groups in randomized clinical trials of adjuvant systemic therapies.

Prognostic significance of accumulation of gene and chromosome alterations and histological grade in node-negative breast carcinoma

The histological grade of atypia is a known prognostic indicator for breast cancer patients and correlates with many gene and chromosome alterations. To investigate the independent prognostic significance of gene and chromosome alterations in axillary node-negative (n0) breast cancers of the invasive ductal and invasive lobular types, the prevalence of eight gene and chromosome alterations and their association with histological grade and recurrence was studied in 129 consecutive patients who had undergone resection over an average follow-up period of 43.4 months. Loss of heterozygosity on 16q, 17p, 16p, 17q and 18q, p53 gene mutation and c-erbB-2 and int-2 gene amplifications were detected in 55%, 37%, 25%, 24%, 22%, 23%, 15% and 11% respectively. Individual alterations in 17p, 17q, 18q, c-erbB-2 and p53 were detected most frequently and gene and chromosome alterations tended to be accumulated in Grade 3 n0 invasive ductal/lobular carcinomas. Histological grade, 18q, int-2 and the number of these gene and chromosome alterations were significant prognostic indicators on Cox's univariate proportional hazard model, and 18q and int-2 were still significant after adjustment for histological grade. Results suggested that examination of the presence of certain gene and chromosome alterations, as well as histological grade, were effective in identifying n0 breast cancer patients at high risk of early recurrence.

Cloning of human chromosome 17-specific cDNAs using representational difference analysis and human-mouse hybrid cells

We employed cDNA representational difference analysis (RDA) with human-mouse somatic hybrid cells containing human chromosome 17 and obtained several cDNA clones specific for this chromosome. A cDNA library from PHA-stimulated T cells was screened with unknown cDNA clones obtained by RDA as probes. Subsequently, 1 complete gene and 1 partial cDNA clone were obtained. Our successful result implies that this subtractive amplification technique with hybrid cells will be a useful aid in positional cloning in large-spanning regions.

Genomic distribution of 5' TTCCA 3' repeat motif and its diagnostic potential in human Y-chromosome-related anomalies

We have studied genomic distribution of a simple repeat motif 5' TTCCA 3' derived from the DYZ1 fraction of the human Y chromosome employing restriction fragment length polymorphism and in situ hybridization techniques. This has led us to develop a synthetic DNA based genetic marker specific to human genome. Randomly selected human genomic DNA from both sexes, digested with a total of 16 restriction enzymes, OAT20Y probe comprising four repeat units of 5'TTCCA 3' motif failed to reveal fragment length polymorphisms. In contrast, with most of the enzymes, several multilocus monomorphic bands and with a few enzymes, smeary signals were detected. In situ hybridization of the OAT20Y probe with human chromosomes revealed grains on the long arm of the Y chromosome, whereas the X-chromosome and autosomes showed random distribution of the grains without any preferential labeling in the centromeric or telomeric regions. The OAT20Y probe uncovers a 3.4 kb isomorphic band exclusively in the human male DNA digested with Hae III enzyme. Using the OAT20Y probe, we have detected the presence of Y chromosome in mosaic cell populations of Turner's patients with dysgenetic gonads and high levels of LS/FSH. The presence of Y chromosome in these patients has been associated with an increased risk of gonadoblastoma. The OAT20Y probe offers sensitivity and accuracy for the detection of Y-chromosome-bearing cells in a mosaic cell population and, consequently, help in better management of the patients.

Loss of heterozygosity on chromosome 17 and mutation of the p53 gene in retinoblastoma

Loss of heterozygosity (LOH) on chromosome 17 and mutations of the p53 gene were examined in 25 retinoblastomas (RB), consisting of three familial tumors, nine hereditary tumors without family history, 11 non-hereditary tumors, one recurrent tumor and one lung-metastatic tumor. LOH on chromosome 17 was detected in only one of the 23 primary RB. No mutations of the p53 gene were detected in the primary tumors. A recurrent tumor showed LOH on the short arm region of chromosome 17. LOH on chromosome 17 and a point mutation of the p53 gene were also detected in a metastatic tumor. These results suggest that LOH on chromosome 17 and mutation of the p53 gene may not be associated with the development of primary RB, but may play a role in the progression of RB.

The Japan Society of Human Genetics Award Lecture. Application of DNA markers to clinical genetics

DNA technology using DNA sequence polymorphisms has brought a new system to the fields of medicine and forensic science, especially for the studies of genetic diseases and tumor suppressor genes, and for identification of individuals for forensic purpose. Linkage analysis based on segregation of polymorphic alleles in affected families has contributed to identification of many genetic disease. We isolated a large number of polymorphic DNA markers, called VNTR (variable number of tandem repeat) markers and identified the APC gene that is responsible for familial adenomatous polyposis (FAP) by means of a so-called "positional cloning" and characterized germline and somatic mutations of the APC gene in colorectal cancer patients. In addition, we have applied genetic information during colorectal carcinogenesis to sensitive diagnosis of lymph-node metastasis of colorectal cancer.

p53 expression in four human medulloblastoma-derived cell lines

p53 is a tumor suppressor gene found on the short arm of chromosome 17. Loss of one p53 allele and alteration of the other is found in a variety of tumors, including highgrade glial tumors. Point mutations in the remaining allele occur in a highly conserved region of the gene encompassing exons 5-8. Although 40-50% of medulloblastomas lose sequences on the short arm of chromosome 17, alteration of p53 in these tumors is infrequent. To further characterize genetic alteration of p53 in medulloblastoma, we performed a mutational analysis of four medulloblastoma-derived cell lines established by our laboratory. Using two variable-number tandem repeat markers which map distally to p53, we found evidence indicating loss of sequences on the distal end of chromosome 17p in all four lines. However, no gross alterations of the p53 gene were detected. Northern analysis revealed expression of equivalent amounts of full-length p53 messenger RNA in each cell line. Using the polymerase chain reaction to amplify exons 5-8 of the p53 gene, we directly sequenced the amplified fragments and detected no mutations in any of the cell lines. Our results demonstrate that loss of p53 function through gene deletion and/or recessive mutation is not required for growth in our cell lines.

DNA methylation patterns in human tissues of uniparental origin using a zinc-finger gene (ZNF127) from the Angelman/Prader-Willi region

In order to further our understanding of the epigenetic modifications of DNA and its role in imprinting, we examined DNA methylation patterns of human tissues of uniparental origin. We used complete hydatidiform moles (CHM), which are totally androgenetic conceptions, to examine the paternal methylation pattern in the absence of a maternal contribution and we used ovarian teratomas to represent the maternal counterpart. We carried out an analysis of DNA methylation of a gene which has been shown to contain sites which are differentially methylated in a parent-specific fashion. The gene, ZNF127, is located on chromosome 15q11-q13 in the region associated with Prader-Willi and Angelman syndromes. The parent-of-origin DNA methylation has been postulated to reflect the presence of an imprint and recent studies have confirmed that ZNF127 is differentially expressed only from the paternal chromosome. We identified a unique pattern of hyper- and hypomethylated sites in androgenetic conceptions which was nearly identical to the paternal pattern found in sperm. This may represent the paternal germ-line methylation imprint. We also studied partial hydatidiform moles, non-molar triploid conceptions, normal chorionic villi, and somatic tissue. These all demonstrated a modified DNA methylation pattern characteristic of normal chorionic villi with only limited findings of the imprint. Our results suggest that human androgenetic conceptions may provide an excellent model to analyze epigenetic DNA modifications, such as methylation, in imprinted genes. The paternal allele-specific methylation imprint will also be useful clinically to confirm the androgenetic nature of suspected molar conceptions in which parental blood samples may not be available.

Comparative mapping of the barley genome with male and female recombination-derived, doubled haploid populations

Male (anther culture) and female (Hordeum bulbosum) derived, doubled haploid populations were used to map the barley genome and thus determine the different recombination rates occurring during meiosis in the F1 hybrid donor plants. The anther culture-derived (male recombination) population showed an 18% overall increase in recombination rate. This increased recombination rate was observed for every chromosome and most of the chromosome arms. Examination of linkage distances between individual markers revealed eight segments with significantly higher recombination in the anther culture-derived population, and one in the Hordeum bulbosum-derived population. Very strong distortions of single locus segregations were observed in the anther culture-derived population, but map distances were not affected significantly by these distortions. There were 1.047 and 0.912 recombinations per chromosome in the anther culture and Hordeum bulbosum-derived doubled haploid populations, respectively.

p53 mutation in epithelial ovarian carcinoma and borderline ovarian tumor

We have investigated a series of 19 human ovarian carcinomas and 17 borderline ovarian tumors to determine the loss of heterozygosity on chromosome 17p and possible concurrent p53 mutations. Allelic losses were assessed using restriction fragment length polymorphism study, and p53 gene mutations were detected by single strand conformation polymorphism analysis and by direct sequencing. In addition, we stained the same tumor sections immunohistochemically to detect p53 protein in tissues. Among 19 ovarian malignant tumor samples tested, we identified 17p allelic deletions in 12 (63.2%) of 19 informative cases. The p53 gene mutation was observed in 7 of 19 (36.8%) malignant ovarian tumors, and it was predominantly observed in tumors with allelic loss on 17p (six of seven tumors, 85.7%). Although 9 cases of 17 borderline ovarian tumors showed shifted bands on single strand conformation polymorphism analysis, only one case was proved to have a point mutation in direct sequencing. We also obtained six cases (31.6%) of positive immunoreactivity from 19 ovarian cancers and 3 cases (17.6%) from 17 borderline ovarian tumors. We conclude that loss or inactivation of tumor suppressor gene function by chromosome 17p allelic deletions or p53 mutations are important genetic changes in ovarian cancer.

Identification of an unbalanced cryptic translocation t(9;17)(q34.3;p13.3) in a child with dysmorphic features

We report a case of an unbalanced cryptic telomeric translocation 46,XY,der(17),t(9;17)(q34.3;p13.3) in a boy with dysmorphic features and developmental delay. The proband had intrauterine growth retardation, postnatal short stature, and mild microcephaly. Magnetic resonance imaging showed incomplete myelination, but no evidence of lissencephaly. Cytogenetic analysis of the proband's peripheral blood showed an abnormal 17p. Fluorescence in situ hybridisation (FISH) with a Miller-Dieker cosmid probe did not detect a deletion for that area. Further analysis with a 17p telomere specific probe identified an unbalanced telomeric translocation. The same probe was used to determine the presence of an apparent balanced translocation t(9;17)(q34.3;p13.3) in the mother of the proband. The balanced translocation was confirmed with two cosmids that map distally on 9q34.3. Two phenotypically normal half sibs, a maternal aunt, a maternal uncle, and the maternal grandmother were found to be balanced translocation carriers as well. A subtle translocation carriers as well. A subtle translocation is one mechanism that can produce an abnormal phenotype in a patient who had a normal karyotype at lower band resolution levels.

p53 gene alterations in special types of breast carcinoma: a molecular and immunohistochemical study in archival material

The p53 locus on the short arm of chromosome 17 at 17p13.1 was examined for small genomic deletions and mutations in 23 formalin-fixed, paraffin-embedded cases of special types of breast carcinoma (six medullary, seven apocrine, five differentiated tubular, and five papillary). p53 mutations in the evolutionarily conserved exons 5-9 were detected in 11 cases (four apocrine, two papillary, two medullary, and three differentiated tubular), using the novel non-radioactive PCR-based Hydrolink mutation detection enhancement (MDE) method, and confirmed by direct sequencing of the PCR products. Missense mutations causing amino acid substitutions were evenly distributed among exons. One case of apocrine carcinoma showed a polymorphism at codon 213 (CGA-->CGG). Twelve out of 23 cases were found to express a strong nuclear signal against CM-1 and DO-7, two anti-p53-specific antibodies. Small genomic deletions in the vicinity of the p53 locus were detected in 11 tumours (three papillary, three differentiated tubular, two medullary, and three apocrine carcinomas), using the multiplex PCR method. No statistical correlation was found between deletions at 17p13.1 and p53 mutations (P < 0.5). In addition, p53 mutations and immunoexpression correlated with the c-erbB-2 gene product, an oncogenic protein that has been implicated in cell cycle control (P < 0.001). Our findings suggest that genomic alterations of the p53 gene are quite common events associated with special types of breast carcinoma, particularly of the apocrine subtype, but the prognostic value is unlikely to be of clinical importance.

Colorectal carcinomas show frequent allelic loss on the long arm of chromosome 17 with evidence for a specific target region

Allelic loss is a common mechanism of inactivation of tumour-suppressor genes in colorectal carcinomas. A number of known or putative tumour-suppressor genes including NF1, BRCA1, NME1, NME2 and prohibitin are present on the long arm of chromosome 17, and this region has not been extensively analysed in colorectal tumours. In this study 72 colorectal carcinomas were examined for allelic loss at eight loci on chromosome 17. Allelic loss was frequent both at the p53 locus, which is known to be important in colorectal carcinoma, and also telomeric to p53 on 17p. Allelic loss continued to be present in more than 50% of cases in the pericentromeric region and on proximal 17q to the marker LEW101 (D17S40) at 17q22-23. The most telomeric markers on 17q showed lower rates of allelic loss. Analysis of cases with partial deletions which did not include the p53 locus showed a common region of overlap of the deletions centred on D17S40. This suggests the target of allelic loss on 17q is a tumour-suppressor gene in this region.

Loss of heterozygosity on the short arm of chromosome 17 in uterine cervical carcinomas

DNA samples from 26 cervical carcinoma and normal tissue pairs were studied by restriction fragment length polymorphism (RFLP) analysis to determine the frequency of loss of heterozygosity (LOH) on 17p. Allelic loss in the p13.1 region of chromosome 17, known to contain the TP53 locus, was not detected in any of 10 informative cases. Instead, LOH was detected on 17p13.3 in eight (40%) of 20 informative cases with at least one of two 17p13.3 markers. Examination of the intragenic region of p53 in the same samples using polymerase chain reaction (PCR)-RFLP analysis showed no LOH in the gene (none of 16 informative individuals).

Association among p53 gene mutation, nuclear accumulation of the p53 protein and aggressive phenotypes in breast cancer

In order to reveal whether differences in the type and site of p53 gene mutations influence the function of the gene and tumor phenotype, we examined nuclear accumulation of the p53 protein immunohistochemically, loss of the other p53 allele by restriction-fragment-length polymorphism analysis, and histological grade of atypia in 52 breast-cancer tissue specimens in which the position and pattern of the mutation were identified. When mis-sense point mutations or deletions of 3n bases (n = 1, 2, ...), which did not cause a frameshift downstream, occurred within codons 110-180 or 234-285, containing highly conserved regions, the p53 protein was almost always (92%) accumulated in nuclei in a majority of the cancer cells. When these mutations occurred outside these regions, only 46% of the cases showed nuclear accumulation of the protein in a majority of cancer cells. In tumors with non-sense point mutations or deletion of 3n + 1 or 3n + 2 bases (n = 0, 1, 2, ...), which caused a downstream frameshift, nuclear accumulation of the p53 protein was absent in 93% of cases. Irrespective of the mutation site or pattern, a majority of cases showing p53 mutation revealed loss of heterozygosity on 17p13 (83%), which suggested they do not carry wild-type p53 allele, and the highest histological grade of atypia (90%). Regardless of differences in their protein-expression pattern, a majority of the p53 gene mutations were suggested to function in a recessive mode and to be involved in the development of histologically aggressive breast cancer.

Detailed analysis of loss of heterozygosity on chromosome band 17p13 in breast carcinoma on the basis of a high-resolution physical map with 29 markers

We have constructed a physical map of chromosome band 17p13, using 29 markers that had been localized to 17p13 by means of fluorescence in situ hybridization (FISH) and analysis by pulsed-field gel electrophoresis (PFGE). The map spans nearly 8 Mb of genomic DNA, and the estimated average distance between each marker is roughly 290 kb. The p13 band of chromosome 17 is thought to contain a putative tumor suppressor gene in addition and distal to TP53. Deletion mapping in a large number of breast carcinomas indicated that the tumor suppressor gene lies between the loci defined by cC117-708 (D17S878) and p144D6 (D17S34), which are an estimated 7 Mb apart. Our results should contribute to construction of a contig map of chromosome band 17p13 with cosmid and/or YAC (yeast artificial chromosome) clones, and to isolation of the putative tumor suppressor gene.

Genetic alterations on chromosome 17 in human breast cancer: relationships to clinical features and DNA ploidy

We analyzed DNA from 105 primary breast cancers to assess amplification of the ERBB2 gene and loss of heterozygosity (LOH) on chromosome 17 using 4 polymorphic markers, and investigated the relationships of these genetic alterations to clinicopathological characteristics including DNA ploidy. Amplification of the ERBB2 gene was observed in 28% of the tumors. ERBB2 was amplified in tumors of all clinical stages and amplification was significantly linked to lymph node metastasis. LOH at D17S5 was observed in 28 of 57 informative tumors, while 17 of 62 informative tumors showed allelic loss at TP53. Among the 37 tumors informative for both loci, 32% showed LOH at these loci and 49% retained both alleles, indicating that there was a significant relationship between LOH at D17S5 and at TP53. We also examined LOH at the D17S74 and NME1 loci on chromosome 17q. LOH at D17S74 and NME1 was observed in 20% and 22% of the informative tumors, respectively, but there was no significant association between LOH at these loci. Of the 4 loci tested, LOH at TP53, D17S74, and NME1 was associated with clinical stage. Lymph node metastasis was correlated with LOH at NME1. Moreover, allelic loss was more frequent in aneuploid tumors than in diploid tumors. These results suggest that certain combinations of genetic alterations on chromosome 17 may cooperate in the development and/or progression of breast cancer. Furthermore, it seems likely that analysis of these alterations in breast cancer patients may provide useful prognostic information.

Hemizygosity at the elastin locus in a developmental disorder, Williams syndrome

Williams syndrome (WS) is a developmental disorder affecting connective tissue and the central nervous system. A common feature of WS, supravalvular aortic stenosis, is also a distinct autosomal dominant disorder caused by mutations in the elastin gene. In this study, we identified hemizygosity at the elastin locus using genetic analyses in four familial and five sporadic cases of WS. Fluorescent in situ hybridization and quantitative Southern analyses confirmed these findings, demonstrating inherited and de novo deletions of the elastin gene. These data indicate that deletions involving one elastin allele cause WS and implicate elastin hemizygosity in the pathogenesis of the disease.

Evidence for linkage of the gene causing familial Mediterranean fever to chromosome 17q in non-Ashkenazi Jewish families: second locus or type I error?

Familial Mediterranean fever (FMF) is an autosomal recessive disorder of unknown pathogenesis, characterized by recurrent, self-limited attacks of fever with synovitis, peritonitis, or pleurisy. Using DNAs from affected Israeli families, we have recently mapped the gene causing FMF (designated MEF) to the short arm of chromosome 16, with two-point lod scores in excess of 20. In this report we consider the possibility of a second FMF susceptibility locus. Before discovering linkage to markers on chromosome 16, we had found suggestive evidence for linkage to chromosome 17q, with the following maximal two-point lod scores: D17S74 (pCMM86), Z = 2.47, (theta = 0.20); D17S40 (pLEW101), Z = 2.15 (theta = 0.15); D17S35 (CRI-pP3-1), Z = 1.78 (theta = 0.15); D17S46 (pLEW108), Z = 1.69 (theta = 0.18), D17S254, Z = 2.30 (theta = 0.20). Moreover, multipoint linkage analysis using D17S74 and D17S40 as fixed loci gave Z = 3.27 approximately 10 centimorgans (cM) telomeric to D17S40. Data with the chromosome 17 markers alone in our families suggested locus heterogeneity. Nevertheless, our families were not separable into complementary subsets showing linkage either to chromosome 16 or to chromosome 17. We also examined the possibility that the positive lod scores for chromosome 17 might reflect a secondary, modifying locus. By several measures of disease severity, families with positive lod scores for chromosome 17 loci had no worse disease than those with negative lod scores for these loci. We conclude that chromosome 17 does not encode a major FMF susceptibility gene for some of the families, nor does it encode a disease-modifying gene. Rather, it would appear that linkage to chromosome 17 is a "false positive" (type I) error. These results reemphasize the fact that a lod score of 3.0 corresponds to a posterior probability of linkage of 95%, with an attendant 1 in 20 chance of observing a false positive.

Molecular genetic evidence for the delineation of a more severe form of familial adenomatous polyposis which results from fresh mutation

Familial adenomatous polyposis, an inherited pre-malignant condition, is caused by mutation in the adenomatous polyposis coli (APC) gene at chromosome 5q22. The lifetime risk of carcinoma approaches 100%, with an average age at death from cancer of 40 years, allowing most patients to complete reproduction. Since there is no evidence for a rising incidence, this is at variance with an apparently high mutation rate. We present evidence for the delineation of a severe form, which hitherto has largely been maintained by fresh mutation. An atypically high frequency of loss of heterozygosity at chromosome 5q22 in small adenomas correlated with an early age of onset or malignancy in two patients, both due to fresh mutation. In both cases, the mutation in APC was shown to be a commonly occurring deletion, leading us to postulate the co-existence of a modifying gene.

Genetic polymorphism of the single locus probes pL159-1 and pL355-8

The genetic polymorphism of the single-locus probes pL159-1 (D18S17) and pL355-8 (D20S15) was investigated in 445 unrelated individuals using PstI as restriction enzyme. Fragment size calculations were obtained using the molecular weight size marker MW-SBH. The basic relationship between migration distance and molecular weight was transformed using an exponential function. Fragment size frequency data show 2 peaks for pL159-1 at 4.36kb (2.36%) and 4.67 kb (6.29%) and one peak for pL355-8 at 6.04 kb (5.73%). The rate of heterozygosity exceeded 70% for both probes.

Different cytotoxic and mutagenic responses induced by X-rays in two human lymphoblastoid cell lines derived from a single donor

Two human lymphoblastoid cell lineages derived from the same parental line exhibit markedly different survival and mutational responses to X-irradiation, but not to chemical point mutagens. WI-L2-NS (ATCC CRL 8155) and TK6 (ATCC CRL 8015) both are derived from the original WI-L2 isolate described by Levy et al. (1968). Both lines are near diploid with stable and indistinguishable karyotypes (47, X, Y 13 +). However, differences in the extent of heterozygosity of chromosome 17 RFLP markers have been detected in these lines. Relative to TK6, WI-L2-NS and several cell lines subsequently derived from it exhibit enhanced survival after X-ray treatment. This is due partly to a more pronounced shoulder in the dose response curve for WI-L2-NS and partly to a higher D0 than is observed in TK6. X-ray-induced mutant frequencies also are markedly different. At the hprt locus, the overall magnitude of the response is similar in the two cell lines. However, in TK6, a linear equation appears to be the best fit to the data, as compared to a linear quadratic curve for WI-L2-NS. Induced mutant frequencies at the tk locus in heterozygotes derived from WI-L2-NS are 20-50-fold higher than those seen in TK6 and tk heterozygous derivatives of TK6. Analysis of the mutability of the two tk alleles in various tk heterozygotes of WI-L2-NS reveals a similar pattern to that described previously in heterozygotes derived from TK6; 3 times as many mutants were recovered from one tk allele than the other. A possible explanation for the higher survival and induced mutant frequencies seen in WI-L2-NS and its derivatives is the presence in these lines of an error prone repair system not functioning in TK6.

p53 oncogene mutations in three human prostate cancer cell lines

p53 gene structure and chromosome 17p alleles were studied in the three human prostate cancer cell lines, LNCaP, DU-145, and PC-3. Our laboratory has two separate culture lines of the LNCaP human prostate cancer cells. One strain, LNCaP-GW, had a mutation in one of two alleles at position 273 (arg > his). This mutation could not be detected in a second strain of LNCaP, LNCaP-ATCC. Immunohistochemical staining for P53 protein in the cell lines indicated that protein overexpression in LNCaP was heterogeneous, even in clonal isolates derived from LNCaP-GW that contained the codon 273 mutation in every cell. We also performed in vitro and in vivo growth analysis to compare the LNCaP-GW and LNCaP-ATCC cells. LNCaP-GW grew more rapidly than LNCaP-ATCC in vitro. However, LNCaP-ATCC formed tumors efficiently when inoculated into nude mice, whereas LNCaP-GW formed tumors much less efficiently. Consideration must be given to the notion that some of these p53 mutations arose during in vitro passage. We also confirmed published findings with two other human prostate cancer cell lines. In DU-145, two mutations were found in the p53 gene. A mutation at codon 274 (pro > leu) and a second mutation at codon 223 (val > phe) were present. PC-3 cells were hemizygous for chromosome 17p. The single copy of the p53 gene had a base pair deletion at codon 138 that generated a frame shift and a new in-frame stop codon at position 169.

Linkage studies of Usher syndrome type 1: exclusion results from the Usher syndrome consortium

Usher Syndrome Type 1 is an autosomal recessive disease characterized by profound congenital hearing impairement and vestibular dysfunction followed by the onset of retinitis pigmentosa in childhood or early adolescence. Members of the Usher Syndrome Consortium, whose objective is to locate and isolate the genes for Usher syndrome, have pooled linkage data from 36 families with 111 affected individuals. We report the analysis of 206 blood group, protein, and DNA marker polymorphisms. No evidence of linkage heterogeneity among families was found for any of the markers studied; the negative lod scores exclude the locus for this disease from about 39% of the genome. Our results indicate the regions of the genome to which our continuing efforts should be directed.

Allelic loss of chromosome 17p in urothelial cancer: strong association with invasive phenotype

Allelic loss of chromosome 17p with a mutated p53 gene on the remaining allele has been observed in various kinds of human cancers. To examine the significance of allelic loss of chromosome 17p in human urothelial cancer with special attention to the clinicopathological features, 49 tumors with various stages and grades from 43 cases (35 bladder cancers and 8 renal pelvic or ureteral cancers) were examined for loss of heterozygosity using 5 polymorphic probes on chromosome 17p. Thirty-seven cases were informative, and allelic loss of chromosome 17p was observed in 15 (41%) of them. In bladder cancers, the loss of 17p was observed with significantly higher frequency (p < 0.01) in cases with invasive (> or = pT2) tumors (7/10, 70%) than in cases with superficial (pTa or pT1) tumors (4/21, 19%). In renal pelvic or ureteral cancers, none of 2 superficial tumors and all of 4 invasive tumors showed the allelic loss. As to tumor grade, the allelic loss was observed in 1/9 (11%) for grade 1 cases, 6/18 (33%) for grade 2 cases, and 8/10 (80%) grade 3 cases (grade 1 versus 3, p < 0.01; grade 2 versus 3, p < 0.05). On the other hand, examination of clinical features, such as primary tumor site, tumor multiplicity or previous history of urothelial cancer did not significantly influence the frequency of the allelic loss. Our results suggest that the allelic loss of chromosome 17p is strongly associated with invasive phenotype in urothelial cancer. The results further indicate that the 17p deletion may represent a new genetic marker of malignant potentials in urothelial cancers.

The use of PCR to help quantify the protection provided by impregnated bednets

Bednets impregnated with a pyrethroid insecticide are an important recent advance in malaria vector control. Here, Suzanne Gokool, Deborah Smith and Chris Curtis describe how a combination of field work with specially designed huts and DNA fingerprinting of mosquito bloodmeals can be used to help assess whether impregnated bednets would give sufficient protection to prevent infection in areas of intense malaria transmission.

X rays induce interallelic homologous recombination at the human thymidine kinase gene

We have developed a human lymphoblast cell line for the study of interchromosomal homologous recombination at the endogenous thymidine kinase (tk) gene on chromosome 17 (M. B. Benjamin, H. Potter, D. W. Yandell, and J. B. Little, Proc. Natl. Acad. Sci. USA 88:6652-6656, 1991). This cell line (designated 6:86) carries unique heterozygous frameshift mutations in exons 4 and 7 of its endogenous tk alleles and can revert to TK+ by frame-restoring mutations, gene conversion, or reciprocal recombination. Line 6:86 reverts spontaneously to TK+ at a frequency of 10(-7) to 10(-8), and exposures to X-irradiation or the frameshift mutagen ICR-191 induce increased reversion frequencies in a dose-dependent manner. Another cell line (designated 4:2) carries a homozygous exon 7 frameshift and is not expected to revert through mechanisms other than frame-restoring mutation. Line 4:2 reverts to TK+ at a lower spontaneous frequency than does 6:86 but can be induced with similar kinetics by ICR-191. In contrast to line 6:86, however, X rays did not induce detectable reversion of line 4:2. We have characterized a number of 6:86-derived revertants by means of restriction fragment length polymorphism analysis at tk and linked loci, single-strand conformation polymorphisms, and direct transcript sequencing. For X rays, most revertants retain both original mutations in the genomic DNA, and a subset of these frameshift-retaining revertants produce frameshift-free message, indicating that reversion is the result of reciprocal recombination within the tk gene. Frame-restoring point mutations, restoration of original sequences, and phenocopy reversion by acquisition of aminopterin resistance were also found among X-ray-induced revertants, whereas the ICR-191-induced revertants examined show only loss of the exon 7 frameshift.

X rays induce interallelic homologous recombination at the human thymidine kinase gene

We have developed a human lymphoblast cell line for the study of interchromosomal homologous recombination at the endogenous thymidine kinase (tk) gene on chromosome 17 (M. B. Benjamin, H. Potter, D. W. Yandell, and J. B. Little, Proc. Natl. Acad. Sci. USA 88:6652-6656, 1991). This cell line (designated 6:86) carries unique heterozygous frameshift mutations in exons 4 and 7 of its endogenous tk alleles and can revert to TK+ by frame-restoring mutations, gene conversion, or reciprocal recombination. Line 6:86 reverts spontaneously to TK+ at a frequency of 10(-7) to 10(-8), and exposures to X-irradiation or the frameshift mutagen ICR-191 induce increased reversion frequencies in a dose-dependent manner. Another cell line (designated 4:2) carries a homozygous exon 7 frameshift and is not expected to revert through mechanisms other than frame-restoring mutation. Line 4:2 reverts to TK+ at a lower spontaneous frequency than does 6:86 but can be induced with similar kinetics by ICR-191. In contrast to line 6:86, however, X rays did not induce detectable reversion of line 4:2. We have characterized a number of 6:86-derived revertants by means of restriction fragment length polymorphism analysis at tk and linked loci, single-strand conformation polymorphisms, and direct transcript sequencing. For X rays, most revertants retain both original mutations in the genomic DNA, and a subset of these frameshift-retaining revertants produce frameshift-free message, indicating that reversion is the result of reciprocal recombination within the tk gene. Frame-restoring point mutations, restoration of original sequences, and phenocopy reversion by acquisition of aminopterin resistance were also found among X-ray-induced revertants, whereas the ICR-191-induced revertants examined show only loss of the exon 7 frameshift.

An attempt to define sets of cooperating genetic alterations in human breast cancer

The extent and the variation of losses of genetic material were examined in a series of 191 human breast cancers by means of a set of 18 polymorphic DNA probes, specific of 7 chromosomal arms (1p, 1q, 3p, 11p, 13q, 17p and 18q) known to be frequently affected by allele losses. Frequencies of losses of heterozygosity ranged from a low of 3.5% (chromosome 13q) to a high of 27% (chromosome 3p). The number of sites involved in breast cancer added to the frequent occurrence of concomitant losses at several chromosomal arms within the same tumor suggest cooperative effects of these LOHs. We were therefore interested in assessing the existence of preferential associations between sets of LOHs in our panel of tumors. Statistically significant associations were found between LOHs at chromosomes 1p and 17p, and between LOHs at chromosomes 11p and 17p. Furthermore, since all the tumors presently studied had previously been analyzed for proto-oncogene amplification at 5 distinct chromosomal sites, we tested for associations between LOH and DNA amplification. Such associations were indeed observed as exemplified by the correlations observed between the LOH at 11p and amplification of the erbB2 gene and LOH at 17p and the amplification of the flg gene. The only correlation with clinico-pathological parameters that could be observed linked the occurrence of LOHs on 11p with recurrent breast cancer (p = 0.015). Sets of several LOHs or LOHs and gene amplifications could not be significantly related to any marker of tumor aggressiveness.

CEPH maps

There are CEPH genetic maps on each homologous human chromosome pair. Genotypes for these maps have been generated in 88 laboratories that receive DNA from a reference panel of large nuclear pedigrees/families supplied by the Centre d'Etude du Polymorphisme Humain. These maps serve as useful tools for the localization of both disease genes and other genes of interest.

Loss of NF1 alleles in phaeochromocytomas from patients with type I neurofibromatosis

Type I neurofibromatosis (NF1) is a common autosomal dominant disorder that affects tissues derived from the neural crest. The manifestations are varied, comprising generalised disorders of growth and development as well as an increased risk of benign and malignant tumours including phaeochromocytomas and neurofibrosarcomas. The NF1 locus has been mapped to chromosome bands 17q11-12, and recently the NF1 gene has been cloned. Deletions identified in the constitutional genotype of some patients have suggested that the NF1 phenotype may arise from loss of function mutations of the NF1 gene, consistent with the hypothesis that it is a tumour suppressor gene. To date, however, analysis of NF1 tumours has not revealed the frequent allele losses encompassing the NF1 locus, implying loss of the wild-type NF1 allele, which would support this hypothesis. We report allele losses with markers flanking the NF1 region in each of 7 NF1 phaeochromocytomas. In each of the 3 tumours for which this could be determined, the loss involved the wild-type chromosome. These results provide strong evidence that, in cells of the adrenal medulla at least, the NFI gene may act as a tumour suppressor.

Gene dosage is a mechanism for Charcot-Marie-Tooth disease type 1A

Charcot-Marie-Tooth disease type 1A (CMT1A) is the most common inherited peripheral neuropathy in humans, characterized electrophysiologically by decreased nerve conduction velocities (NCVs). CMT1A is associated with a large submicroscopic DNA duplication in proximal 17p. In this report we demonstrate that a patient with a cytogenetically visible duplication, dup(17)(p11.2p12), has decreased NCV. Molecular analysis demonstrated this patient was duplicated for all the DNA markers duplicated in CMT1A as well as markers both proximal and distal to the CMT1A duplication. These data support the hypothesis that the CMT1A phenotype can result from a gene dosage effect.

Absence of linkage between the angiotensin converting enzyme locus and human essential hypertension

The angiotensin converting enzyme (ACE) is a key component of the renin angiotensin system that contributes to the regulation of blood pressure (BP). Recent demonstration of linkage between the ACE locus and elevated BP in a rat model of hypertension has further emphasized ACE as a candidate gene in human hypertension. We report the localization of the ACE gene on the genetic map of chromosome 17, and identify an extremely polymorphic marker at the human growth hormone (hGH) locus which shows no recombination with ACE. We have found no evidence to support linkage between the ACE locus and hypertension, which suggests that mutations at the ACE locus do not commonly contribute to the pathogenesis of hypertension in our test population.

Isolation of region-specific cosmids from chromosome 5 by hybridization with microdissection clones

A method is described for the isolation of chromosome region specific cosmids. The 5q35 region of the long arm of human chromosome 5 was microdissected, digested with MboI, ligated to oligonucleotide adaptors, amplified by the polymerase chain reaction and cloned into a plasmid vector. Inserts which did not contain highly repetitive sequences were used to screen a chromosome 5 cosmid library by direct hybridization. There were 33 positive cosmid clones identified with 4 microclones. Individual cosmid clones were biotinylated and used as probes for fluorescence in situ hybridization to metaphase chromosomes. Of the 33 cosmids that were mapped, 29 localized to q35 and 4 to q34, demonstrating the specificity of the microdissection library and the cosmids.

Variation in genomic Alu repeat density as a basis for rapid construction of low resolution physical maps of human chromosomes

Human DNA restriction fragments containing high numbers of Alu repeat sequences can be preferentially detected in the presence of other human DNA restriction fragments in DNA from human: rodent somatic cell hybrids when the DNA is fragmented with enzymes that cleave mammalian DNA infrequently. This ability to lower the observed human DNA complexity allowed us to develop an approach to order rapidly somatic hybrid cell lines retaining overlapping human genomic domains. The ordering process also generates a relative physical map of the human fragments detected with Alu probe DNA. This process can generate physical mapping information for human genomic domains as large as an entire chromosome (100,000 kb). The strategy is demonstrated by ordering Alu-detected NotI fragments in a panel of mouse: human hybrid cells that span the entire long arm of human chromosome 17.

p53 allele losses, mutations and expression in breast cancer and their relationship to clinico-pathological parameters

The p53 locus on the short arm of chromosome 17 at 17p 13.1 was examined for loss of heterozygosity, mutation, mRNA and protein expression in 60 primary breast cancers. Allele loss around the p53 locus was detected in 19/45 informative tumours (42%). p53 mutations in the evolutionarily conserved exons 5 to 9 were detected in 17/60 (28%) by amplification mismatch and confirmed by direct DNA sequencing. p53 mRNA expression was detected by Northern blot in 36/59 (61%) of tumours, and p53 protein expression using antibody 1801 on frozen-tissue sections in 13/44 of the tumours examined. p53 mutation was significantly associated with oestrogen-receptor-poor tumours (p less than 0.01) and hence with poor prognosis, but not with other clinical or pathological parameters. There was no statistical correlation between loss of heterozygosity around the p53 locus at 17p13.1 and p53 mutation. Furthermore, p53 mutation was not associated with p53 expression detected by immunohistochemical staining with antibody 1801 or as p53 mRNA. In addition, events on 17p (allele losses, p53 mutation, p53 expression) were independent of c-erbB-2 expression. In breast cancer, by contrast with colorectal, lung and ovarian cancer, there appears to be no clear association between p53 DNA abnormalities and p53 expression.

Molecular mechanisms of spontaneous and induced loss of heterozygosity in human cells in vitro

The human TK6 lymphoblast cell line is heteroallelic at the thymidine kinase (TK) locus, with one functional and one nonfunctional allele. Cells that have undergone loss of heterozygosity (LOH) at TK can be selected and cloned in an in vitro assay. In order to study the extent of LOH, we have analyzed a total of 166 thymidine kinase-deficient mutants that arose either spontaneously or following induction by X-ray or ethyl methane sulfonate (EMS) using DNA probes in and around the TK gene on chromosome 17. Two distinct groups of mutants with different doubling times were identified. Among slow-growth mutants, the predominant change for both spontaneous and induced mutants was LOH that generally extended through the entire TK gene to both proximal and distal markers on 17q. While the majority of both spontaneous and X-ray-induced normal-growth mutants showed LOH, this was considerably more localized in scale for X-ray-induced mutants, which rarely involved the distal marker. LOH was rare among EMS-induced normal-growth mutants. LOH was never observed with a 17p marker, indicating that nondisjunctional events were not involved in any of the mutant clones examined. Densitometric analysis of the LOH mutants indicated mitotic recombination was a likely mechanism in more than half the spontaneous LOH mutants in both groups, whereas most induced mutants appeared to arise from simple deletions.

Overexpression of the p53 protein and allele loss at 17p13 in ovarian carcinoma

Mouse monoclonal antibodies PAb 240 and PAb 1801 which specifically immunoprecipitate p53 protein, were used to examine 27 fresh ovarian tumours (16 serous adenocarcinomas, six endometrioid carcinomas, one mucinous adenocarcinoma, one mucinous borderline tumour and three benign adenomas). Eleven out of 16 (69%) serous adenocarcinomas and one endometrioid tumour showed positive staining with one or both antibodies and none of the mucinous or benign tumours stained with either antibody. DNA from tumour and peripheral blood leukocytes was used to identify allelic deletions on chromosome 17p in tumours. 11/12 positively staining tumours showed less of heterozygosity (LOH) on 17p at the nearest informative locus to the p53 gene. In this series of ovarian tumours, LOH on 17p correlates closely with the aberrant expression of the p53 protein in a high proportion of advanced stage serous adenocarcinomas. This observation suggests that the p53 tumour suppressor gene is involved in the evolution of epithelial ovarian cancer (EOC) and may have prognostic significance.

A map of 22 loci on human chromosome 22

We constructed a genetic linkage map of the entire long arm of human chromosome 22 with 30 polymorphic markers, defining 22 loci. The map consists of a continuous linkage group 110 cM long, when male and female recombination fractions are combined; average distance between the loci is 5.2 cM. All loci were placed on the map with high support against alternative orders (odds in excess of 1000:1). The order of loci presented in our map is in full agreement with that of the previous linkage maps of chromosome 22 and with the physical assignment of markers. Two markers included in this map, KI-831 (D22S212) and pEFZ31 (D22S32), allowed us to better define the region of the (11;22) translocation breakpoint specific for Ewing sarcoma. Ten additional polymorphic markers were placed on the 22-loci map with odds lower than 1000:1 against alternative locations. In total, we have introduced 29 new markers on the linkage map of chromosome 22.

A genetic linkage map of 41 restriction fragment length polymorphism markers for human chromosome 3

A genetic linkage map for human chromosome 3 has been constructed using 41 polymorphic DNA markers genotyped in 40 CEPH reference families. The map spans a genetic distance of 261 cM in males and 413 cM in females; the ratio of these distances (approximately 1.6 in favor of female meioses) was fairly constant across the map. Frequency of recombination was relatively uniform throughout much of the chromosome, except that in both telomeric regions recombination was more frequent than the physical distances would predict. The genetic map was basically in agreement with physical localization of 24 loci that were mapped by fluorescent in situ hybridization. This map can be used for linkage studies for genetic diseases, and it will serve as a step toward a high-resolution map for human chromosome 3.

TP53 gene mutations and 17p deletions in human astrocytomas

Astrocytomas, including the most malignant form, glioblastoma multiforme, are the most frequent and deadly primary tumors of the human nervous system. Recent molecular genetic analyses of astrocytomas have demonstrated frequent chromosome 17 deletions involving the telomeric region of the short arm (17p12-pter). This region contains a candidate tumor suppressor gene, TP53, which has recently been implicated in the etiology of a broad array of human cancers. To study the possible role of TP53 in astrocytoma development, 24 randomly chosen human astrocytic tumors were examined for genomic TP53 sequence aberrations using primer-directed DNA amplification in conjunction with direct sequencing. Five of the 11 grade III astrocytomas (glioblastoma multiforme), but only one of seven grade II astrocytomas (anaplastic astrocytoma) and none of either the grade I astrocytomas or oligodendrogliomas demonstrated distinct point mutations involving the TP53 gene. These data suggest that TP53 mutations may play a role in astrocytoma development and are predominantly associated with higher grade tumors.

A system for assaying homologous recombination at the endogenous human thymidine kinase gene

A system for assaying human interchromosomal recombination in vitro was developed, using a cell line containing two different mutant thymidine kinase genes (TK) on chromosomes 17. Heteroalleles were generated in the TK+/+ parent B-lymphoblast cell line WIL-2 by repeated exposure to the alkylating nitrogen mustard ICR-191, which preferentially causes +1 or -1 frameshifts. Resulting TK-/- mutants were selected in medium containing the toxic thymidine analog trifluorothymidine. Mutations were characterized by exon-specific polymerase chain reaction amplification and direct sequencing. In two lines, heterozygous frameshifts were located in exons 4 and 7 of the TK gene separated by approximately 8 kilobases. These lines undergo spontaneous reversion to TK+ at a frequency of less than 10(-7), and revertants can be selected in cytidine/hypoxanthine/aminopterin/thymidine medium. The nature and location of these heteroallelic mutations make large deletions, rearrangements, nondisjunction, and reduplication unlikely mechanisms for reversion to TK+. The mode of reversion to TK+ was specifically assessed by DNA sequencing, use of single-strand conformation polymorphisms, and analysis of various restriction fragment length polymorphisms (RFLPs) linked to the TK gene on chromosome 17. Our data suggest that a proportion of revertants has undergone recombination and gene conversion at the TK locus, with concomitant loss of frameshifts and allele loss at linked RFLPs. Models are presented for the origin of two recombinants.

DNA duplication associated with Charcot-Marie-Tooth disease type 1A

Charcot-Marie-tooth disease type 1A (CMT1A) was localized by genetic mapping to a 3 cM interval on human chromosome 17p. DNA markers within this interval revealed a duplication that is completely linked and associated with CMT1A. The duplication was demonstrated in affected individuals by the presence of three alleles at a highly polymorphic locus, by dosage differences at RFLP alleles, and by two-color fluorescence in situ hybridization. Pulsed-field gel electrophoresis of genomic DNA from patients of different ethnic origins showed a novel SacII fragment of 500 kb associated with CMT1A. A severely affected CMT1A offspring from a mating between two affected individuals was demonstrated to have this duplication present on each chromosome 17. We have demonstrated that failure to recognize the molecular duplication can lead to misinterpretation of marker genotypes for affected individuals, identification of false recombinants, and incorrect localization of the disease locus.