Polymerase Chain Reaction-single Strand Conformation Research Articles

Genotoxic Effects of Benzo[a]pyrene and Dibenzo[a,l]pyrene in a Human Lung Cell Line

Several studies have shown that polycyclic aromatic hydrocarbons (PAHs) produce genotoxic effects in assays performed in vivo and in vitro. This study was undertaken to investigate the ability of benzo[a]pyrene (BP) and dibenzo[a,l]pyrene (DBP) to induce DNA damage in a human lung fibroblast cell line (MRC-5), using sister-chromatid exchanges test (SCEs), the comet assay, and evaluating point mutations in codon 12 of the K-ras protooncogene by polymerase chain reaction-single-strand conformation polymorphisms (PCR-SSCPs) and restriction fragment length polymorphisms (RFLP)-enriched PCR methods. Sister-chromatid exchanges frequencies were significantly increased in cells exposed to benzo[a]pyrene and dibenzo[a,l]pyrene in relation to controls (p < .001). Using the standard alkaline comet assay, significant differences between groups were found for the variable comet moment (CM) when cells were exposed to BP (p < .001) and DBP (p < .001). Nevertheless, PCR-SSCP and RFLP-enriched PCR methods did not show any association between treatments with BP and DBP and K-ras point mutations. The data presented in this study indicated that BP and DBP induced both DNA strand breaks and sister-chromatid exchanges but not significant point mutations at codon 12 of K-ras gene in the MRC-5 cell line.

EGFR intragenic loss and gene amplification in astrocytic gliomas

We have studied EGFR gene amplification and allelic status of chromosome 7 in 68 tumors consisting of 34 WHO grade IV glioblastomas (26 primary and 8 secondary), 14 WHO grade III anaplastic astrocytomas, and 20 WHO grade II astrocytomas, by polymerase chain reaction–single-strand conformation polymorphism (PCR-SSCP), quantitative PCR, and microsatellite analysis. EGFR gene amplification was present in 27 of these tumors (40%), and we identified allelic losses at 7p11∼p14 in 38 of the 68 cases (56%), including 17 tumors displaying loss for EGFR intragenic markers. The positive correlation ( P < 0.05, χ 2) between tumors with EGFR intragenic loss and EGFR gene amplification, frequently displaying the EGFR vIII form, suggests that EGFR gene rearrangement leading to intragenic loss is a molecular event that participates in the amplification process of this gene.

Molecular analysis of unknown β-globin gene mutations using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique and its application in Thai families with β-thalassemias and β-globin variants

Objectives: Approximately 40 β-globin gene mutations have been identified in Thailand. The detection of these mutations is currently performed by the reverse dot blot (RDB) hybridization technique, which could detect only known mutations. We describe here the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) assay for detecting unknown mutations of the β-globin genes. Design and methods: Six PCR fragments covering the promoter, entire coding region, and intervening sequences were amplified before separation by the SSCP technique. Fifteen known mutations and two polymorphisms were analyzed by this technique in various gel mixtures and temperatures to compare their mobility shift patterns. Results: The clear patterns of mobility shift were demonstrated when a 10% polyacrylamide gel with 5% glycerol was used. The sensitivity was found to be 100% when electrophoreses were performed at both room temperature and 6°C. This technique was then applied to screen β-globin gene mutations in Thai families with similar profiles of abnormal hemoglobins. The distinct patterns of mobility shifts were observed in which further sequencing analysis revealed an AC insertion at codon 146, causing hemoglobin Tak. Conclusion: The PCR-SSCP technique might be a useful molecular technique to minimize the requirement of direct genomic sequencing to identify β-globin gene mutations and could be applied in several developing countries where resources are limited but genetic hemoglobin disorders are highly prevalent.

Constitutional and Somatic RB1 Mutation Spectrum in Nonfamilial Unilateral and Bilateral Retinoblastoma in India

An epidemiologic survey has indicated a comparatively high prevalence of retinoblastoma (Rb) in Asian countries. Recently, the development of preventive strategies in nonfamilial Rb has become a major goal. The present studies were designed for identification and characterization of constitutional and somatic RB1 gene mutations by conventional cytogenetics, fluorescent in situ hybridization (FISH) and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP)-DNA sequencing. Of 34 patients 32 were nonfamilial and 2 were familial Rb. Maternal inheritance of del (13q14) was common. FISH was sensitive in detecting monoallelic RB1 deletion/deletion mosaicism as a first genetic hit in 20% of cases. Somatic and germline RB1 point mutations affected exons 3, 17, 20, and 21 and these were identified as novel mutations. Involvement of exon 20 as a predisposing mutation in sporadic unilateral retinoblastoma (URB) probably suggests the susceptibility of exon 20 to unknown etiologic factors in our population. A de novo RB1 deletion along with transmitted RB1 point mutation from an asymptomatic parent was identified as a unique predisposing RB1 mutation chimerism in a URB case that later evolved to bilateral retinoblastoma (BRB). The predisposing mutations such as del (13q), RB1 mono-allelic deletion and RB1 point mutation in sporadic Rb were de novo as well as transmitted mutations from asymptomatic/symptomatic parents. The RB1 mutation incidence was comparatively higher (25%) in nonfamilial Rb with emphasis on high prevalence in sporadic URB (18% versus 0%-9% in the literature series). The present studies demonstrated the efficacy of a multitechnique approach to detect various types of constitutional RB1 mutations such as RB1 deletion, deletion mosaicism, point mutation, mutation chimerism in patients of symptomatic/asymptomatic parents.

No association between a 3’ untranslated region polymorphism in the neprilysin gene and Alzheimer's disease in the Japanese population

AbstractBackground: Alzheimer's disease (AD) is caused by neuronal cell death with aggregation of amyloid‐β (Aβ) in the brain cortex and hippocampus. Neprilysin (NEP) plays an important role mainly in the degradation of Aβ. The NEP‐knockout mouse shows low degradation of Aβ and is confirmed to have AD. The frequency of the C/C genotype of NEP159 C/T polymorphism in the 3’ untranslated region (UTR) of the NEP gene Apolipoprotein E (Apo E) ɛ4 group has been reported to be higher than that of the control group. In the present study, we screened for the polymorphism in our Japanese AD and control subjects. Furthermore, we searched for a new polymorphism in exon 1 and exon 24 in the NEP gene.Methods: 121 sporadic AD (SAD) patients were recruited from among the inpatients and outpatients of the hospital the authors work in. The 101 age‐matched control subjects were recruited from healthy volunteers with no history of dementia or other neuropsychiatric diseases. The NEP159 C/T polymorphism and Apo E were genotyped by the polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) method and a new polymorphism was detected by the polymerase chain reaction–single strand conformation polymorphism (PCR–SSCP) method.Results: We confirmed that the frequency of the Apo E ɛ4‐allele was higher in the SAD group than in the control group. There was no significant difference in genotypic distribution of the NEP159 C/T polymorphism between the control and SAD groups.Conclusion: Our studies suggest that there is no genetic association between the NEP159 C/T polymorphism and the risk of Japanese SAD. Our results indicate that further genetic studies of the NEP gene should be performed in other ethnic groups.

Do cancer cells selectively mutate HFE to increase their intracellular iron?

Malignant cells compared to their normal counter-parts, have an increased requirement for iron in order to achieve an enhanced cell growth. Transferrin receptor (TfR), an essential transport protein that enables cells to satisfy their need of iron, is upregulated in cancer cells. The hemochromatosis gene (HFE) produces a protein that interacts with TfR; and we hypothesized that tumor cells would selectively mutate HFE to improve their iron-uptake and thus provide themselves a growth advantage over non-tumor cells. A total of 36 non-small cell lung cancer (NSCLC) samples and matched tumor-free tissue from the same individuals were examined for HFE mutations using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). Sequencing analysis of the shifted bands in three of 36 cases (in both, the tumor and matching normal tissue of the same individuals) revealed the cysteine to tyrosine substitution at amino acid residue 282 (C282Y) in the protein. Surprisingly, matching samples from one patient with a heterozygous C282Y mutation in the germline, showed loss of heterozygosity in the tumor sample at the mutant HFE allele resulting in loss of the C282Y and retention of the normal allele. In addition, we examined 45 tumor cell lines from 11 different tissues. Five cell lines had a heterozygous mutation of HFE, none had a homozygous HFE mutation in the coding region. In summary, our experiments suggest that HFE mutations are not associated with a growth advantage for cancer cells.

Analysis of the 11β-Hydroxysteroid Dehydrogenase Type 2 Gene (HSD11B2) in Human Essential Hypertension

The HSD11B2 gene, encoding the kidney isoenzyme 11beta-hydroxysteroid dehydrogenase, is a candidate for essential hypertension. We previously showed that the frequency of shorter alleles of a CA repeat polymorphism in the first intron of 11beta-HSD2 gene was significantly higher among salt-sensitive than salt-resistant individuals with hypertension. The aim of the study was to analyze the HSD11B2 gene to assess whether some of its variants might be involved in hypertension. Exons 2, 3, 4, and 5 were screened by polymerase chain reaction-single-strand conformation polymorphism analysis in 292 hypertensive patients and 163 control subjects. The samples with variant electrophoretic patterns at single-strand conformation polymorphism were re-analyzed using an automated DNA sequencer. A case-control study was then performed by comparing genotype frequencies in hypertensive and normotensive subjects. Analysis of the HSD11B2 showed that in hypertensive patients there is a higher prevalence of two associated polymorphisms, Thr156/Thr(C468A) in exon 2 (ex2) and Glu178/Glu(G534A) in exon 3 (ex3), than in normotensive subjects (9% v 2.4%). This association did not correlate with salt sensitivity. C468A alone correlates significantly with hypertension (9%) and was identified only in 3% of control subjects (P < .05), whereas G534A was identified also in about 7% of normotensive subjects. The urinary free cortisol/urinary free cortisone ratio (UFF/UFE) was significantly higher in hypertensive patients compared with control subjects (P < .01). Two different polymorphisms of the HSD11B2 gene were observed. The association of both polymorphisms was significantly higher in hypertensive subjects than in control subjects. Its role should be further investigated, but it could be related to other mutations in the promoter region of HSD11B2 or to the modulation of 11beta-HSD2 mRNA processing in hypertensive subjects.

Bone morphogenetic protein receptor IB as a candidate gene for prolificacy in Small Tail Han and Hu ewes

AbstractThe bone morphogenetic protein receptor IB (BMPR-IB) gene, which controls the fecundity of Booroola Merino ewes, was studied as a candidate gene for the prolificacy of Small Tail Han and Hu ewes. A single nucleotide polymorphism of the BMPR-IB gene was detected in both high (Small Tail Han and Hu) and low (Suffolk and Dorset) fecundity sheep breeds by polymerase chain reaction–single-strand conformation polymorphism (PCR-SSCP) analysis. The results indicated the presence of the same mutation (A746G) of the BMPR-IB gene in both Small Tail Han and Hu ewes and in Booroola Merino ewes, but not in both Suffolk and Dorset ewes. In Small Tail Han ewes, frequencies of BB, B+ and ++ genotypes were 0.524, 0.383 and 0.093, respectively. In Hu ewes, these frequencies were 0.882, 0.118 and 0.000. The BMPR-IB genotype distributions were significantly different (P&lt;0.001) among high- and low-fecundity sheep breeds. Small Tail Han ewes with genotype BB had 0.92 (P&lt;0.01) and 1.02 (P&lt;0.01) lambs more than those with genotype ++ in the first and second parity, respectively. These results demonstrated that the BMPR-IB gene is a major gene affecting the prolificacy in both Small Tail Han and Hu ewes, and could be used as a molecular genetic marker to select the litter size in sheep.

ERBB2 kinase domain mutation in the lung squamous cell carcinoma

Mounting evidence exists that the activation of proto-oncogene by somatic mutation plays an important roles in the development of human cancers. Recent reports revealed that the kinase domain of ERBB2 gene, a proto-oncogene, is somatically mutated in the lung adenocarcinomas, suggesting the mutated ERBB2 gene may act as an oncogene in human cancers. The purpose of this was to see whether the ERBB2 kinase domain is mutated in other lung cancer types besides the adenocarcinoma. Here, we performed mutational analysis of the ERBB2 kinase domain by polymerase chain reaction-single strand conformation polymorphism assay in 114 non-adenocarcinoma type non-small cell lung cancers (NSCLCs) tissue samples, including 100 squamous cell carcinomas, three adenosquamous carcinomas and 11 large cell carcinomas. We detected the ERBB2 kinase domain mutation in one squamous cell carcinoma (1.0%). The detected ERBB2 mutation showed G to C transversion at bp 2305 (2305G>C), which would result in the substitution of Asp to His at codon 769 (D769H). The amino acid D769 is located in the alpha-helix within the kinase domain, which is important in the binding of ATP with ERBB2. We simultaneously analyzed the somatic mutations of EGFR, K-RAS, PIK3CA and BRAF genes in the squamous cell carcinoma with the ERBB2 mutation, and found that the tumor did not harbor any EGFR or ERBB2 or K-RAS or PIK3CA or BRAF gene mutation, either. This study demonstrated that in addition to lung adenocarcinoma ERBB2 kinase domain mutation could occur in lung squamous cell carcinomas, and suggested that alterations of ERBB2-mediated signaling pathway by ERBB2 mutations may occasionally contribute to the development of lung squamous cell carcinomas.

Analysis of PTEN Gene Mutations in Korean Patients With Cowden Syndrome and Polyposis Syndrome

PTEN (phosphatase and tensin homologue deleted in chromosome 10) is a candidate tumor suppressor gene. Mutations of this gene are responsible for PTEN hamartoma tumor syndromes, including Cowden syndrome, Bannayan-Riley-Ruvalcaba syndrome, Proteus syndrome, and Proteus -like syndromes. Recently, PTEN mutations were identified in several human neoplasms. We analyzed the DNA of various organs and lesions in Korean patients with Cowden syndrome, their family members, and patients with familial adenomatous polyposis for germline or somatic PTEN mutations. The 11 patients included in this study were 5 patients with Cowden syndrome, 4 of their family members, and 2 patients with familial adenomatous polyposis. Deletions and mutations in exons 1 to 9 of the PTEN gene were evaluated by polymerase chain reaction-single strand conformation polymorphism and sequencing analysis in esophageal acanthosis, gastric polyps, colonic polyps, skin lesions, and peripheral blood mononuclear cells. To exclude common polymorphisms, 240 controls were tested. All patients with Cowden syndrome showed several to numerous polyps in the gastrointestinal tract. A missense mutation at codon 217 (GTC to GAC, Val to Asp) in exon 7 was identified in one Cowden syndrome patient, and a nonsense mutation at codon 211 (TGC to TGA, Cys to stop) in exon 6 was identified in a second patient. Identical mutations were found in all tissue samples, including colonic polyps, from each patient. No PTEN mutations were found in their family members or in any patient with familial adenomatous polyposis. None of tested controls contained a mutation. We have identified two new germline PTEN mutations in Korean patients with Cowden syndrome. Mutations in the introns and regulatory regions of the PTEN gene may be present in additional patients with Cowden syndrome and polyposis syndrome.

Novel mutations of PAX9 gene in Chinese patients with oligodontia

To investigate the mutational characteristics of PAX9 gene in Chinese patients with congenital oligodontia and thus to provide a molecular basis for studying the pathogenesis of oligodontia. Thirteen individuals with oligodontia and 9 healthy individuals, from 4 unrelated autosomal dominant families, and 16 sporadic patients with hypodontia in China, as well as 196 healthy control individuals (without oligodontia or hypodontia) were screened. Congenital absence of teeth was confirmed by panoramic X-ray analysis. Mutations of PAX9 gene were detected using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. After the finding of abnormal SSCP bands, analysis was carried out with DNA sequencing. PCR-SSCP detected SSCP bands alteration in exon2 of PAX9 gene in two unrelated families. Sequencing of PAX9 gene revealed a novel frameshift mutation (109InsG) and a novel missense mutation (C139T). All the affected members of each family were heterozygous for the mutations. In sporadic patients and the other two families, no similar sequence changes in PAX9 gene were found. The results extend the spectrum of mutations in PAX9 gene associated with oligodontia. The novel mutations will play an important role in gene diagnosis of oligodontia.

GSTO polymorphism analysis in thyroid nodules suggest that GSTO1 variants do not influence the risk for malignancy

A new class of glutathione S-transferase enzymes named omega (GSTO) has been recently identified and shown to be expressed in a wide range of human tissues. A genetic polymorphism of the GSTO1 gene causing an alanine-to-aspartate (A140D) substitution in amino acid 140 produces a variant with lowered enzyme activities in the biotransformation of inorganic arsenic, a common contaminant of drinking water in many regions of the world and a well-known carcinogen. In order to investigate the role of GSTO1 inheritance pattern on thyroid cancer risk we used a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP)-sequencing approach to compare the genotypes of 173 (87 women, 86 men; 18-81 years old; 47+/-18 years old) healthy control individuals with those of 145 patients with thyroid nodules (84 women, 61 men; 17-81 years old; 49+/-14 years old) including 17 follicular carcinomas, 76 papillary carcinomas, 21 follicular adenomas and 31 multinodular goiters. The incidence of GSTO1 variants was similar in the control population and population with the benign and malignant nodules. There was no association between genotype and the patients' clinical features, tumour parameters of aggressiveness at diagnosis or behaviour during follow-up. We conclude that GSTO1 variants do not influence the risk for thyroid nodules or their pathologic and clinical characteristics.

K-ras mutations in rectal cancer undergone preoperative radiotherapy

To detect K-ras mutations in rectal carcinoma before and after preoperative radiotherapy, and study genetics effect of radiotherapy in rectal cancer. Forty patients with rectal cancer in pTNM stage II or III were enrolled. There were 20 males and 20 females. Sixteen tumours were pTNM II stage, 24 pTNM III. All patients received preoperative adjuvant radiotherapy. The treatment time is 4 weeks for 40 Gy in 2.0 Gy fractions and it is usually followed by an interval of 1-2 weeks before the operation. Tumor tissue and normal mucosa 2, 4, 6 cm to tumor were collected from patients before preoperative adjuvant radiotherapy and after operation. The K-ras mutations in codon 12 were investigated using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) in tumors and normal mucosa. The frequencies of K-ras mutations before preoperative adjuvant radiotherapy in tumor tissue and normal mucosa 2, 4, 6 cm to tumor were 47.5%, 22.5%, 2.5% and 0. The frequencies of K-ras mutations before preoperative adjuvant radiotherapy were higher in tumor tissue than in normal mucosa, and were higher in normal mucosa 2 cm to tumor than 4 cm and 6 cm to tumor. The postoperative frequencies of K-ras mutations in tumor tissue and normal mucosa 2 cm, 4 cm, 6 cm to tumor were 25.0%, 5.0%, 0 and 0. Compared to same locations of control group, the frequency of K-ras mutations in tumor tissue and normal mucosa 2 cm to tumor significantly decreased after radiotherapy. Frequency of K-ras mutations of rectal cancer issue and normal mucosa 2 cm to tumor were significantly higher than other normal rectal mucosa, and decreased significantly after radiotherapy. So radiotherapy can inhibit early events of carcinogenesis of mucosa nearby tumor. It was the potential reason of increased rates of resection and sphincter-saving after radiotherapy.

Genetic analysis of microsomal epoxide hydrolase gene and its association with lung cancer risk

The human microsomal epoxide hydrolase (EH) gene contains polymorphic alleles, which may be linked to increased risk for tobacco-related lung cancer. The purpose of this study is to screen new polymorphisms and determine whether these polymorphisms can be used to predict individual susceptibility to lung cancer. The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis was used to screen for polymorphisms in the coding region of the EH gene. Eleven polymorphisms, including previously reported polymorphisms, were identified and the prevalence of these variants was assessed in at least 50 healthy Caucasians and African-Americans. Among the 11 polymorphisms, the prevalence of the amino acid-changing EH polymorphisms in codons 43, 113 and 139 was examined in 182 Caucasian incident cases with primary lung cancer, as well as in 365 frequency-matched controls to examine the role of EH polymorphisms in lung cancer risk. A significant increase in lung cancer risk was observed for predicted high EH activity genotypes (odds ratio (OR) 2.3, 95% confidence interval (CI) 1.2-4.3) as compared with low EH activity genotypes. This association was more pronounced among patients with lung adenocarcinoma (OR 4.7, 95% CI 1.7-13.1). These results suggest that the EH polymorphism plays an important role in lung cancer risk and is linked to tobacco smoke exposure.

Somatic VHL alteration and its impact on prognosis in patients with clear cell renal cell carcinoma

4602 Backgrounds: Somatic inactivation of the von Hippel-Lindau (VHL) gene is the most frequent genetic event observed in clear cell renal cell carcinomas (CC-RCCs). However, the prognostic relevance of somatic VHL alteration and its target, hypoxia inducible factor (HIF)-1α, has not been defined. We investigated the genetic changes in the VHL gene and HIF-1α and studied their clinical implications in patients with sporadic CC-RCC. Methods: Patients who underwent nephrectomy were eligible if they had pathologically confirmed CC-RCC that was not associated with VHL disease or familial RCC. Tumor tissues were selected from paraffin blocks on the basis of hematoxylin and eosin (H&E)-stained sections. Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis was performed to detect VHL mutations and genetic changes in HIF-1α, which were followed by automated direct sequencing. VHL hypermethylation was examined by methylation-specific PCR. Results: A total of 56 patients were enrolled and somatic VHL alterations were detected in 16 (29%); intragenic mutation in eight, hypermethylation in five, and both alteration in three. The mutation types were missense in five patients, silent in three, nonsense in two, and frameshift in one. Somatic VHL alterations were not significantly associated with progression-free survival (PFS) or overall survival (OS). However, patients with a ‘loss-of-function’ VHL mutation showed significantly decreased PFS (P=0.016) and OS (P=0.046). Although the association between VHL alteration and response to immunotherapy was not significant (P=0.486), The CC-RCCs with missense mutation seem to have had better responses to immunotherapy. The Pro582Ser change in HIF-1α was detected in six patients (11%) and was positively correlated with the development of metastases (P=0.023). Concluions: This study did not show an association between somatic VHL alteration and prognosis in patients with sporadic CC-RCC. However, it suggests that the therapeutic and prognostic implication of somatic VHL alteration may be different according to the mutational subtype and that the Pro582Ser change in HIF-1α may contribute to the development of metastases. No significant financial relationships to disclose.

Somatic VHL alteration and its impact on prognosis in patients with clear cell renal cell carcinoma

Somatic inactivation of the von Hippel-Lindau (VHL) gene is the most frequent genetic event observed in clear cell renal cell carcinoma (CC-RCC). However, the prognostic relevance of somatic VHL alteration and its target, hypoxia inducible factor (HIF)-1alpha has not been defined. We investigated the genetic changes in the VHL gene and HIF-1alpha and studied their clinical implications in patients with sporadic CC-RCC. Patients who underwent nephrectomy were eligible if they had pathologically confirmed CC-RCC not associated with VHL disease or familial RCC. Tumor tissues were selected from paraffin blocks on the basis of hematoxylin and eosin (H&E)-stained sections. Polymerase chain reaction-single strand conformation polymorphism analysis was performed to detect VHL mutations and genetic changes in HIF-1alpha, which were followed by automated direct sequencing. VHL hypermethylation was examined by methylation-specific PCR. A total of 56 patients were enrolled and somatic VHL alterations were detected in 16 patients (29%); intragenic mutation in eight, hypermethylation in five, both alterations in three. The mutation types were missense in five patients, silent in three, nonsense in two, and frameshift in one. Somatic VHL alterations were not significantly associated with progression-free survival (PFS) or overall survival (OS). However, patients with 'loss-of-function' VHL mutation showed significantly decreased PFS (P=0.016) and OS (P=0.046). Although the association between VHL alteration and response to immunotherapy was not significant (P=0.486), patients with missense mutation seem to have better response to immunotherapy. The Pro582Ser change in HIF-1alpha was detected in six patients (11%) and was positively correlated with the development of metastases (P=0.023). This study did not show an association between somatic VHL alteration and prognosis in patients with sporadic CC-RCC. However, it suggests that the therapeutic and prognostic implication of somatic VHL alteration may be different according to the mutational subtype and that the Pro582Ser change in HIF-1alpha may contribute to the development of metastases.

Allelic loss at 10q26 in osteosarcoma in the region of the BUB3 and FGFR2 genes

Loss of heterozygosity at 10q26 was mapped using microsatellite markers in 20 osteosarcomas. A four-megabase region centered on marker D10S587 was affected by allelic loss in 60 percent of osteosarcomas. The most frequently lost marker was D10S1723. Around 15 known genes are found in this region. The gene immediately adjacent to D10S1723 encodes BUB3, an element of the spindle assembly mitotic checkpoint. Loss of BUB3 function could contribute to chromosomal instability. The fibroblast growth factor receptor 2 ( FGFR2) gene is located 2 Mb from the BUB3 gene and has the potential for a role in cancer. Inherited mutations of the FGFR2 gene result in skeletal dysplasias. FGFR2 alterations have also been implicated in gastric cancer. Human genome project data were used to design primers for amplifying FGFR2 in 18 genomic segments and BUB3 in 7 genomic segments. In each case, the segments encompassed coding exons and flanking intron sequences. The primers were used to search for mutations by polymerase chain reaction–single-strand conformation polymorphism (PCR-SSCP). Several shifted bands were detected in the BUB3 exon 3 fragment. Sequencing resolved the BUB3 exon 3 fragment shifts into polymorphisms in intron 2. No mutations of BUB3 or FGFR2 were detected. It remains possible that BUB3 or FGFR2 hemizygosity alone contributes to osteosarcoma, or that one of the genes is cryptically inactivated by a higher-order modification or mutation outside the coding region. There may also be a yet undiscovered tumor suppressor gene in this region.

Polymorphisms of the upstream regulatory region of the major histocompatibility complex DRB genes in domestic horses

Sequence information was obtained on the variation of the ELA-DRB upstream regulatory region (URR) after polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) cloning and sequencing of approximately 220 bp upstream of the first exon of horse DRB genes. The sequence of the proximal URR of equine DRB is composed of highly conserved sequence motifs, showing the presence of the W, X, Y, CAAT and TATA conserved boxes of major histocompatibility complex (MHC) class II promoters. Five different polymorphic horse DRB promoter sequences were detected in five horse breeds. The results demonstrate the existence of polymorphism in the nucleotide sequences of the ELA-DRB URR, located in the functionally important conserved consensus sequences, the X2 box, the Y box and the TATA box, while conservation were observed in X1 and CAAT boxes. The nucleotide diversity among horse URRs was intermediate between that seen within human and mouse DRB promoters, suggesting the existence of another important source of variability in ELA-DRB genes. In addition, phylogenetic comparisons, identity analysis and sequence organization suggested that the reported sequences would correspond to an expressed ELA-DRB locus. However, further information about the functional significance of these promoter polymorphisms will probably be acquired through expression studies on the different sequences.

Founder mutation in familial adenomatous polyposis (FAP) in the Balearic Islands

The incidence of familial adenomatous polyposis (FAP) is approximately 7.4 per 100,000 inhabitants. APC gene mutations have been found in 60–70% of all FAP families, codons 1309 (20%) and 1061 (8%) being known hot-spots. We searched for mutations in the APC gene in a population-based registry of FAP from the Spanish Balearic Islands. Fifty-one members of 12 FAP families registered in the Balearic Islands Cancer Registry were studied; three of them were de novo cases. Mutations in the APC gene were analyzed by polymerase chain reaction–single-strand conformation polymorphism (PCR-SSCP) and sequencing. Haplotype was established by combining intra- and extragenic markers. Mutations in the APC gene were detected in 10 out of 12 (83%) families analyzed. Six families shared the same mutation, a 5-bp deletion at codon 1061 (c.3221_3225delACAAA). Five of the families containing this mutation shared the same haplotype and originated in the same geographic area. The codon 1061 mutation in the APC gene is the most common one in the Balearic Islands. Although this codon is a hot-spot, the haplotype analysis of these families is consistent for the presence of a founder effect of the 5-bp deletion at codon 1061 in FAP families in the Spanish Balearic Islands.

TP53 Mutations and Outcome in Osteosarcoma: A Prospective, Multicenter Study

Mutations of the TP53 gene have been associated with resistance to chemotherapy as well as poor prognosis in many different malignancies. This is the first prospective study of the prognostic value of somatic TP53 mutations in patients with newly diagnosed extremity osteosarcoma. One hundred ninety-six patients with high-grade, nonmetastatic osteosarcoma of the extremities were enrolled from seven tertiary care institutions and observed prospectively for tumor recurrence (median follow-up duration, 44 months). All patients received neoadjuvant or adjuvant chemotherapy and surgery. Tumors were analyzed for the presence of TP53 mutations by polymerase chain reaction single-strand conformation polymorphism analysis and direct DNA sequencing. The association of the status of the TP53 gene with the risk of systemic recurrence was examined using survival analyses with traditional and histologic markers as prognostic factors. Patient age was the only factor that varied with TP53 gene status (P = .05). No relationship was identified between TP53 status and systemic relapse (relative risk, 1.24; P = .41). Analyses based on missense or nonsense mutations gave similar results (P > .10). In multivariate analysis, large (> 9 cm) tumor size (relative risk, 1.9; P = .006) and poor histologic response (< or = 90% necrosis) to chemotherapy (relative risk, 2.14; P = .02) were the only significant independent predictors of systemic outcome. We found no evidence that TP53 mutations predict for development of metastases in patients with high-grade osteosarcoma. Identification of other genes that influence chemotherapy response and clinical outcome in osteosarcoma is needed to facilitate further improvements in patient outcomes.