Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction

Mutation hot spots in the canine herpesvirus thymidine kinase gene

The guanine and cytosine content (GC-content) of alpha-herpesvirus genes are highly variable despite similar genome structures. It is known that drug resistant HSV, which has the genome with a high GC-content (approximately 70%), commonly includes frameshift mutations in homopolymer stretches of guanine (G) and cytosine (C) within the thymidine kinase (TK) gene. However, whether such mutation hotspots exist in the TK gene of canine herpesvirus (CHV) which has a low GC-content was unknown. In this study, we investigated mutations in the TK gene of CHV. CHV was passaged in the presence of iodo-deoxyuridine (IDU), and IDU-resistant clones were isolated. In all IDU-resistant virus clones, mutations in the TK gene were observed. The majority of these mutations were frameshift mutations of an adenine (A) insertion or deletion within either of 2 stretches of eight A's in the TK gene. It was demonstrated that CHV TK mutations frequently occur at a limited number of hot spots within long homopolymer nucleotide stretches.

Novel two-dimensional DNA gel electrophoresis mapping for characterizing complex bacterial communities in environmental samples

Genomic DNA profiles such as denaturing gradient gel electrophoresis (DGGE), temporal temperature gradient gel electrophoresis (TTGE), and single-strand conformation polymorphism (SSCP) have been commonly used to characterize bacterial communities in environmental samples. We recently developed a two-dimensional gel electrophoresis (2-DGE) method with a combination of chain-length polymorphism analysis (CLPA) and DGGE analysis, in order to improve the DNA resolution and resolve complex environmental DNA fragments produced by polymerase chain reaction (PCR) amplification. The 2-DGE method can generate high-resolution DNA separation maps on the basis of the lengths and composition polymorphisms of DNA sequences. It can thus facilitate detailed analyses between bacterial communities in complex environmental systems such as soil or water. For the present paper, we further developed two novel 2-DGE methods using a combination of CLPA and TTGE (or CLPA and SSCP) and here describe their potential application to the characterization of bacterial communities in nature using clustering analyses. The results show that DNA amplicons can undergo more detailed separation by the two new mapping than by their corresponding 1-DGE fingerprints. Our findings also suggest that these two new 2-DGE mapping techniques are more easily carried out than previously described DGGE-based 2-DGE mapping because they do not require a chemical denaturing gradient gel.

Polymorphisms within promoter of Japanese flounder (Paralichthys olivaceus) ovary cytochrome P450-c19 (CYP19a) gene associated with reproductive traits

Cytochrome P450 aromatase, which is encoded by the CYP19a gene, converts androgens to estradiol. Considerable evidence suggests that estrogens play an important role in fish reproductive process. Therefore CYP19a is an excellent candidate gene for reproductive traits. Variants in the promoter of the CYP19a gene might also be involved in the control of aromatase expression and affect regulatory mechanism linking cholesterol metabolism to the synthesis of sex steroids. In this study, nine single-nucleotide polymorphisms (SNPs) were detected with polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP), namely A-680G, G-672A, AGTAGT-649 inserting or deleting, T-623C, C-410A, T7-454A, T-402C, TTTCCAGACTGA-345 inserting or deleting, and G-297C. Nine SNPs within the promoter of the CYP19a gene were tested for association with four reproductive traits [serum testosterone (T), serum 17beta-estradiol (E(2)), hepatosomatic index (HSI), and gonadosomatic index (GSI)] in a population of 50 female Japanese flounder individuals. A locus, P3 (TTTCCAGACTGA-345 inserting or deleting, G-297C), was significantly associated with 17beta-estradiol (E(2)) level (P < 0.05) in female Japanese flounder. In addition, there was significant association between one diplotype based on nine SNPs and reproductive trait. The genetic effect for E(2) level of diplotype D3 was significantly higher than those of other diplotypes (P < 0.05). Results indicate that these genetic effects of those variants on E(2) level may help to explain CYP19a gene status in the reproductive endocrinology of Japanese flounder.

Novel mutations in theSLC12A3gene causing Gitelman's syndrome in Swedes

PURPOSE

Gitelman's syndrome (GS) is an inherited autosomal recessive disorder due to loss of function mutations in the SLC12A3 gene encoding the Na-Cl co-transporter (NCCT), the target of thiazide diuretics. The defective function of the NCCT, which normally is expressed in the apical membrane of the distal convolute tubule in the kidney, leads to mild hypotension, hypokalemia, hyperreninemic hyperaldosteronism, mild metabolic alkalosis, hypomagnesemia and hypocalciuria. Up to now, more than 100 mutations of the SLC12A3 gene have been described in GS patients.

METHODS

We have collected 30 patients from Sweden with a clinical diagnosis of GS and undertaken a mutation screening by SSCP and successive sequencing of the 26 exons and intronic boundaries. Both mutations were identified in most (n = 28, 93%) and at least one mutation was identified in all patients.

RESULTS

We found 22 different mutations evenly distributed throughout the gene, 11 of which have not been described previously. The new variants include 8 missense mutations (Glu68Lys, His69Asn, Argl45His, Vall53Met, Gly230Asp, Gly342Ala, Val677Leu and Gly867Ser), 1 insertion (c.834_835insG on exon 6) and 2 splice-site mutations (c.2667 + lT>G substitution in splicing donor site after exon 22, c.1569-1G>A substitution in the splicing acceptor site before exon 13).

CONCLUSION

In Swedish patients with the clinical features of GS, disease-causing mutations in the SLC12A3 gene were identified in most patients. The spectrum of GS mutations is wide making full mutation screening of the SLC12A3 gene necessary to confirm the diagnosis.

Impact of cystic fibrosis transmembrane conductance regulator gene mutation on the occurrence of chronic pancreatitis in Japanese patients

DNA analyses of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in Japanese patients with idiopathic chronic pancreatitis (ICP) were performed to determine the relationship between the CFTR mutation and ICP. The study included patients with alcoholic pancreatitis (n = 20), patients with ICP (n = 20) and healthy volunteers (controls; n = 110). The poly-T region in intron 8 of the CFTR gene was analysed by direct sequencing. The CFTR coding region was screened using single-strand conformational polymorphism and direct sequencing. In the controls, frequencies of the 5T genotype and 5T allele were 4.5% and 3.6%, respectively. The frequency of the 5T genotype was significantly higher in the ICP group (20%) versus controls, but was not significantly different in alcoholic chronic pancreatitis patients (5%). Thus, the CFTR gene mutation, especially the 5T genotype, appears to have some relationship to ICP prevalence in Japanese patients independent of cystic fibrosis.

A new and simple approach for genotyping Alzheimer's disease presenilin-1 mutant knock-in mice

The use of transgenic mice expressing point mutations demands that the detection of the different alleles is efficient and reliable. In addition, the multiplication of transgenes included in mouse models of human disease underlines the importance of correct controls and the fact that investigators need an accurate and rapid genotyping of the littermates generated. In this study, we demonstrate a powerful alternative for genotyping using presenilin-1 mutant knock-in (PS1M146KI) mice as an example. Mutations in the presenilin-1 (PS1) gene are causally linked to many cases of early-onset inherited Alzheimer's disease (AD). PS1M146VKI mice that express the PS1M146V targeted allele at normal physiological levels and triple-transgenic model (3 x Tg-AD) derived from homozygous PS1M146VKI mice were generated to study the pathogenesis of AD. Genotyping PS1M146VKI line requires many steps and thus a large quantity of DNA. In PS1M146VKI mice, only three nucleotides are modified in the gene. Here we show that this small mutated DNA sequence can affect its secondary structure resulting in altered mobility that can be easily detected on a polyacrylamide gel, by the single-strand conformation polymorphism (SSCP) technique. Our results demonstrate that SSCP is a simple, accurate, repeatable and efficient method for the routine genotyping of this current AD model. This method could be easily applied to other transgenic mice.

Imbalance of G and C contents influences the sensitivity of single-strand conformation polymorphism

After analyzing chicken ATPase6 by single-strand conformation polymorphism (SSCP), we observed two band species. But based on the sequencing results, we found two mutations, and one of them was not detected by SSCP. The primer P2 was designed to detect the additional mutation site, which was not detected by the original primer. And the P2 SSCP results then agreed with the sequencing data. Analysis of the percent of G and C bases and secondary structures indicated that it might be caused by a similar secondary structure which might be resulting from serious imbalance of G and C contents.

PCR-SSCP and sequence analysis of three Odontotermes spp. (order: isoptera; family: termitidae) on the basis of partial 16SrRNA gene

Partial 16S gene fragments were amplified by using specific primers in few species/populations of termites of the genus Odontotermes (Isoptera:Termitidae:Macrotermitinae), and the PCR products were subjected to SSCP analysis. Three haplotypes obtained were subjected to sequencing. The sequences obtained were characterized to see the frequencies of each nucleotide bases. High A + T content was observed. The inter-specific pairwise sequence divergence in Odontotermes spp. ranged from 0% to 4.8% across the entire 16S gene fragment. Identical sequences were found between two populations of O. horni. Individuals of different species having Type-I conformational pattern, i.e. O. obesus (-AI) and O. horni (-MI), as well as Type-II of O. obesus (-UII) and O. bhagwatii (-CHII) had no percent diversity. Phylogenetic trees drawn on the basis of distance Neighbour-joining method revealed clustering of individuals according to their genera and families.

High-throughput detection of highly benzimidazole-resistant allele E198A with mismatch primers in allele-specific real-time polymerase chain reaction

BACKGROUND

A point mutation often confers resistance of organisms against medical drugs and agricultural pesticides. Allele-specific nucleotide polymerase chain reaction (ASPCR) and allele-specific quantitative real-time PCR using SYBR Green (ASQPCR) are widely and effectively applied to detect and monitor this type of resistance. However, the former is unsuitable for high-throughput detection, and the latter often reduces the accuracy of detection.

RESULTS

In order to decrease background amplification, a rapid and high-throughput genotyping method with mismatch primers was developed (ASQPCR-MP) and applied specifically to survey the frequency of the highly benzimidazole-resistant MBC(HR) mutation (E198A) in the beta-tubulin gene of Sclerotinia sclerotiorum (Lib.) de Bary populations. Genomic DNA from 223 sclerotia was analysed. Similar genotype results were also obtained using ASPCR with mismatch primers and a mycelial growth inhibition assay. It was found that ASQPCR-MP clearly differentiated MBC(HR) and benzimidazole-sensitive MBC(S) phenotypes. Moreover, ASQPCR-MP took less than 6 h to complete.

CONCLUSION

ASQPCR-MP appears suitable for large epidemiological studies involving resistant genotypes and requiring high-throughout formats.

Correlation of p53 over-expression and alteration in p53 gene detected by polymerase chain reaction-single strand conformation polymorphism in adenocarcinoma of gastric cancer patients from India

AIM: To study the alterations in p53 gene among Indian gastric cancer patients and to correlate them with the various clinicopathological parameters.

METHODS: A total of 103 gastric cancer patients were included in this study. The p53 alterations were studied by both immunohistochemical method as well as polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) analysis. We only studied four (exon 5, 6, 7, and 8) of the 11 p53 exons. The alterations in p53 were also correlated with respect to various clinicopathological parameters.

RESULTS: Among 103 cases, p53 over-expression and alteration were detected in 37 (35.92%) and 19 (18.44%) cases, respectively. Most of the p53 alterations were found at exon 5 (31.54%), followed by exon 6 (26.31%), exon 7 (21.04%) and exon 8 (21.04%). A significant correlation of p53 over-expression was found with p53 alteration (P = 0.000). Concordance between p53 alteration (as detected by SSCP) and over-expression [as detected by immunohistochemistry (IHC)] was found in 75% cases. We found that IHC-positive/SSCP-negative cases accounted for 21% of cases and IHC-negative/SSCP-positive cases accounted for remaining 4% cases.

CONCLUSION: Our results show that p53 gene mutations are significantly correlated with p53 protein over-expression, with 75% concordance in over-expression and alteration in the p53 gene, but 25% disconcordance also cautions against the assumption that p53 over-expression is always associated with a gene mutation. There may be other mechanisms responsible for stabilization and accumulation of p53 protein with no evidence of gene mutation that reflect an accumulation of a non-mutated protein, or a false negative SSCP result.

Alterations of p16 and p14ARF genes and their 9p21 locus in oral squamous cell carcinoma

The p16 gene encodes a 16-kDa cyclin kinase inhibitor, and the p14ARF gene a 14-kDa protein, which acts as a cell cycle regulator or tumor suppressor in human cancer cells. Both genes are mapped on chromosome 9p21. Previous studies have suggested that the p16 gene has important roles in head and neck squamous cell carcinoma. To clarify carcinogenesis in oral squamous cell carcinoma (OSCC), we examined 44 primary OSCCs for alterations of p16 and p14ARF mRNA expression, the methylation status of the p16 gene promoter, the loss of heterozygosity (LOH) at the 9p21 locus, and p16 and p14ARF gene mutations. Alterations of p16 and p14ARF mRNA expression were seen in 27 (61.4%) of 44 and 10 (22.7%) of 44 of OSCC samples, respectively. Methylation of the p16 gene promoter region was detected in 28 (63.6%) of 44 samples, and LOH at 9p21 locus was found in 30 (68.2%) of 44. p16 and p14ARF gene mutations were observed in 4 (9.0%) of 44 and 2 (4.5%) of 44 samples, respectively. Suspected homozygous deletion (HD) was seen in 9 (20.5%) of 44. All cases except one (97.7%) showed alterations in p16, p14ARF, and their locus. These data indicate that the status of p16 and p14ARF genes in OSCC is frequently influenced by methylation, gene mutation, and allelic deletions. Furthermore, these genes and their 9p21 locus have various roles in the pathogenesis of OSCC.

Estimation of SNP allele frequencies by SSCP analysis of pooled DNA

The single strand conformation polymorphism (SSCP) method is a sensitive technique used to detect subtle sequence differences in PCR-amplified DNA fragments as separated peaks in electrophoretic analysis. In this chapter, we focus on SSCP analysis for quantifying polymorphic alleles rather than scanning for mutations. Short fragments carrying single nucleotide polymorphisms are amplified from individual and pooled DNA samples, then the products are labeled with fluorescent dyes and analyzed by automated capillary electrophoresis under nondenaturing conditions. Dedicated software, QSNPlite, interprets trace data of the electrophoresis to identify alleles of individuals and quantify these alleles in the pool. The software can also incorporate sequencing data to assign alleles at the nucleotide level. The procedures described here are being used in association studies that compare allele frequencies between cases and controls to identify genes responsible for common diseases.

Basic molecular techniques for the detection of single nucleotide polymorphisms: genome-wide applications in search for endocrine tumor related genes

The necessity of genotyping high number of variations in extended sample sets has become apparent in the era of large genomic studies of common complex disorders, in cancer and in pharmacogenomics. The single nucleotide polymorphisms' (SNPs) apparent advantages over other genetic markers such as high frequency, relative stability, and statistically random distribution across the genome have made them a method of choice for most of these genome-wide oriented applications. The requirement for simultaneous genotyping of high number of SNPs, keeping at the same time reasonable price and reliable accuracy, triggered the rise of the genotyping throughput, and led to the development of the array-based technologies. The present chapter briefly reviews the methodological and historical aspect of the basic SNP detecting techniques that lie in the basis of the modern high-throughput technologies, providing at the same time detailed guide on the application of one of the most advanced SNP microarray platform on the market: the genome-wide SNP Array 6.0 recently developed by Affymetrix, which we have used to study families with Catney complex and Micronodular adrenocortical hyperplasia. In addition, we discuss practical clues and tips aiming at extending applications and improving performance.

Analysis of population structures of viral isolates using single-strand conformation polymorphism method

The analysis of viral populations requires the use of techniques that describe characteristics of individuals. The single-strand conformation polymorphism (SSCP) makes possible the identification of genetic differences between viral sequences and constitutes an alternative to the expensive and time-consuming cloning and sequencing strategies. Applied to small genomic regions (from 100 to 500 bases in length), SSCP patterns could describe, under appropriate experimental conditions, single nucleotide variations in the studied sequence. The different steps of a complete SSCP procedure, from sampling to pattern analysis (including nucleic acid extraction, RT-PCR amplification, double-stranded DNA quantification, polyacrylamide gel preparation, electrophoresis conditions, and staining procedures), are described using a region (500 bases) of the barley yellow dwarfvirus-PAV (BYDV-PAV, Luteovirus) genome as molecular target.

Structural analysis of point mutations in the Hairless gene and their association with the activity of the Hairless protein

The Notch signaling pathway (NSP) is an important intercellular communication mechanism that regulates embryo development and adult physiological functions. The Hairless (H) protein is a powerful antagonist of the NSP by its interaction with the Suppressor of Hairless (Su[H]) protein, recruiting the corepressors Gro and CtBP. In the present work, we examined the role of several important amino acids in different H protein domains analyzing four mutant lines of Drosophila melanogaster. The mutant alleles were evaluated by single-strand conformational polymorphism (SSCP) analysis and we located mutated regions at different positions along the sequence of the Hairless gene.

Identification of two novel arylsulfatase A mutations with a polymorphism as a cause of metachromatic leukodystrophy

OBJECTIVE

Metachromatic leukodystrophy is a lysosomal storage disorder caused by the deficiency of arylsulfatase A or saposin B. Enzyme deficiency leads to the accumulation of sulfatide, which results in severe demyelination.

METHODS

In this study, clinically suspected patients were diagnosed as metachromatic leukodystrophy by enzyme analysis using p-nitrocathecol sulfate as substrate. Eight exons and flanking regions of arylsulfatase A gene of patients were amplified by polymerase chain reaction and then subjected to single stranded conformational polymorphism analysis. Polymerase chain reaction products of suspicious exons in single stranded conformational polymorphism were purified from agarose gel and sequenced.

RESULTS

DNA sequencing revealed two novel disease-causing missense mutations: the first one is 1568G-->A, 307Glu-->Lys in exon 5 which is together with a 2161C-->T, 391Thr-->Ser polymorphism in exon 7; and the second one is 1603G-->T, 318Trp-->Cys in exon 5.

DISCUSSION

These two mutations are in highly conserved structural elements region of the arylsulfatase A protein. Thus, missense mutations 307Glu-->Lys in exon 5 and 318Trp-->Lys in exon 5 probably change the active site conformation by disrupting the sixth alpha helix and the twelfth beta-sheet structure of the arylsulfatase A protein, respectively, and cause deficiency in enzyme activity. This study provides the molecular basis for understanding the mechanism underlying metachromatic leukodystrophy.

Identification of a single nucleotide polymorphism in porcine testis cytochrome P450-c17 (CYP17) and its effect on steroidogenesis

Raising uncastrated male pigs could have significant economic benefits for pig production. Uncastrated male pigs can accumulate high levels of 16-androstene steroids, however, resulting in boar taint, which is highly objectionable to consumers. Cytochrome P450-c17 (CYP17) interacts with cytochrome b5 in the biosynthesis of the 16-androstene steroids and the sex steroids from pregnenolone. Amino acid substitutions in CYP17 could therefore affect the ability of this enzyme to catalyze the reactions leading to the production of androstenone and the sex steroids. In this study, we established a sensitive and flexible single-stranded conformational polymorphism technique capable of detecting a single nucleotide polymorphism. We then used this method to identify a substitution from T to A at nucleotide 1317 of CYP17, which caused a change in the amino acid sequence from Leu(439) to His(439). This mutation, however, did not alter the enzyme activity of CYP17 in the biosynthesis of androstenone or sex steroids. Other polymorphisms previously suggested for CYP17, which are vital for the functional interaction of CYP17 with CYB5 in human, were not observed. This study suggests that the synthesis of androstenone in pig testis is not directly affected by any polymorphisms in the coding region of the porcine CYP17 gene.

Patched-one or smoothened gene mutations are infrequent in chondrosarcoma

Constitutive hedgehog signaling has been implicated in the tumorigenesis of cartilaginous neoplasia; however, a common mutational mechanism remains unknown. Some tumors exhibiting hedgehog pathway activation such as basal cell cancer frequently harbor PATCHED-ONE (PTCH-1) or SMOOTHENED (SMO) gene mutations. We therefore asked whether mutations of the hedgehog receptor genes PTCH-1 or SMO occur in cartilage tumors. Singlestrand conformation polymorphism (SSCP) analysis with subsequent manual sequencing was performed to detect alterations of PTCH-1 and SMO in 46 cartilage tumors. SSCP detected five shifts in the PTCH-1 gene and two shifts in SMO. Direct DNA sequencing revealed the five shifts in PTCH-1 were caused by silent nucleotide alterations. The two SMO shifts were the result of the same missense mutation (783G>A) and occurred in one dedifferentiated chondrosarcoma and a synovial chondromatosis. The patient with chondromatosis also carried this same mutation in the germline. However, this mutation was also identified in leukocyte DNA from three of 127 (2.4%) control subjects without cartilage tumors, suggesting it may represent a rare SMO variant. Constitutive activation of the hedgehog signaling pathway in chondrosarcoma is rarely caused by PTCH-1 or SMO mutations. [corrected]

Spectrum of novel mutations in the human PKLR gene in pyruvate kinase-deficient Indian patients with heterogeneous clinical phenotypes

Eighteen unrelated pyruvate kinase (PK)-deficient Indian patients were identified in the past 4 years with varied clinical phenotypes ranging from a mild chronic haemolytic anaemia to a severe transfusion-dependent disorder. We identified 17 different mutations in the PKLR gene among the 36 mutated alleles. Ten novel mutations were identified: 427G>A, 499C>A, 1072G>A, 1180G>T, 1216G>A, 1220A>G, 644delG, IVS5 (+20) C>A, IVS9 (+44) C>T, and IVS9 (+93) A>C. A severe syndrome was commonly associated with some mutations, 992A>G, 1436G>A, 1220A>G, 644delG and IVS9 (+93) A>C, in the PKLR gene. Molecular graphics analysis of human red blood cell PK (RPK), based on the crystal structure of human PK, shows that mutations located near the substrate or fructose 1,6-diphosphate binding site may change the conformation of the active site, resulting in very low PK activity and severe clinical symptoms. The mutations target distinct regions of RPK structure, including domain interfaces and catalytic and allosteric sites. In particular, the 1216G>A and 1219G>A mutations significantly affect the interdomain interaction because they are located near the catalytic site in the A/B interface domains. The most frequent mutations in the Indian population appear to be 1436G>A (19.44%), followed by 1456C>T (16.66%) and 992A>G (16.66%). This is the first study to correlate the clinical profile with the molecular defects causing PK deficiency from India where 10 novel mutations that produce non-spherocytic haemolytic anaemia were identified.

Polymorphisms at the GLUT2 (β-cell/liver) glucose transporter gene and non-insulin-dependent diabetes mellitus (NIDDM): analysis in affected pedigree members

The precise genetic defects underlying the etiology of non-insulin-dependent diabetes mellitus (NIDDM) have yet to be identified. The beta-cell/liver glucose transporter gene GLUT2 represents a good candidate for the etiology of the disease, being involved in the glucose signalling for beta-cell insulin release. Population association studies of the GLUT2 gene in NIDDM have so far yielded controversial results. In order to determine the possible contribution of this gene to the inheritance of NIDDM, we have employed a new approach, where two polymorphic markers of the GLUT2 locus, detected with the restriction enzyme Taq-1, were examined for linkage with the disease in a group of 22 Italian pedigrees with affected members (n = 50). Departure from independent segregation between markers and disease was analyzed by the Affected-Pedigree-Members (APM) statistical method. Furthermore, association analysis between the Taq-1 RFLPs at the GLUT2 locus and NIDDM was performed in a group of diabetics with a strong family history, comprising the 22 probands and 23 other diabetics with an affected first-degree relative. The results indicate that there was no segregation distortion between the Taq-1 markers of the GLUT2 gene and the disease in the pedigrees examined. Also, no significant difference in genotype distribution, haplotype and allele frequencies was found between diabetics and controls for the two Taq-1 RFLPs. We conclude that genetic variation at the GLUT2 transporter gene is unlikely to contribute in a major way to the inheritance for NIDDM in this Italian population.

Involvement of TSC genes and differential expression of other members of the mTOR signaling pathway in oral squamous cell carcinoma

Background

Despite extensive research, the five-year survival rate of oral squamous cell carcinoma (OSCC) patients has not improved. Effective treatment of OSCC requires the identification of molecular targets and signaling pathways to design appropriate therapeutic strategies. Several genes from the mTOR signaling pathway are known to be dysregulated in a wide spectrum of cancers. However, not much is known about the involvement of this pathway in tumorigenesis of OSCC. We therefore investigated the role of the tumor suppressor genes, TSC1 and TSC2, and other members of this pathway in tumorigenesis of OSCC.

Methods

Expression of genes at the RNA and protein levels was examined by semi-quantitative RT-PCR and western blot analyses, respectively. Loss of heterozygosity was studied using matched blood and tumor DNA samples and microsatellite markers from the TSC1, TSC2 and PTEN candidate regions. The effect of promoter methylation on TSC gene expression was studied by treating cells with methyltransferase inhibitor 5-azacytidine. Methylation status of the TSC2 promoter in tissue samples was examined by combined bisulfite restriction analysis (COBRA).

Results

The semi-quantitative RT-PCR analysis showed downregulation of TSC1, TSC2, EIF4EBP1 and PTEN, and upregulation of PIK3C2A, AKT1, PDPK1, RHEB, FRAP1, RPS6KB1, EIF4E and RPS6 in tumors. A similar observation was made for AKT1 and RPS6KB1 expression in tumors at the protein level. Investigation of the mechanism of downregulation of TSC genes identified LOH in 36.96% and 39.13% of the tumors at the TSC1 and TSC2 loci, respectively. No mutation was found in TSC genes. A low LOH rate of 13% was observed at the PTEN locus. Treatment of an OSCC cell line with the methyltransferase inhibitor 5-azacytidine showed a significant increase in the expression of TSC genes, suggesting methylation of their promoters. However, the 5-azacytidine treatment of non-OSCC HeLa cells showed a significant increase in the expression of the TSC2 gene only. In order to confirm the results in patient tumor samples, the methylation status of the TSC2 gene promoter was examined by COBRA. The results suggested promoter hypermethylation as an important mechanism for its downregulation. No correlation was found between the presence or absence of LOH at the TSC1 and TSC2 loci in 50 primary tumors to their clinicopathological variables such as age, sex, T classification, stage, grade, histology, tobacco habits and lymph node metastasis.

Conclusion

Our study suggests the involvement of TSC genes and other members of the mTOR signaling pathway in the pathogenesis of OSCC. LOH and promoter methylation are two important mechanisms for downregulation of TSC genes. We suggest that known inhibitors of this pathway could be evaluated for the treatment of OSCC.

Mutation detection using ENDO1: application to disease diagnostics in humans and TILLING and Eco-TILLING in plants

BACKGROUND

Most enzymatic mutation detection methods are based on the cleavage of heteroduplex DNA by a mismatch-specific endonuclease at mismatch sites and the analysis of the digestion product on a DNA sequencer. Important limitations of these methods are the availability of a mismatch-specific endonuclease, their sensitivity in detecting one allele in pool of DNA, the cost of the analysis and the ease by which the technique could be implemented in a standard molecular biology laboratory.

RESULTS

The co-agroinfiltration of ENDO1 and p19 constructs into N. benthamiana leaves allowed high level of transient expression of a mismatch-specific and sensitive endonuclease, ENDO1 from Arabidopsis thaliana. We demonstrate the broad range of uses of the produced enzyme in detection of mutations. In human, we report the diagnosis of the G1691A mutation in Leiden factor-V gene associated with venous thrombosis and the fingerprinting of HIV-1 quasispecies in patients subjected to antiretroviral treatments. In plants, we report the use of ENDO1 system for detection of mutant alleles of Retinoblastoma-related gene by TILLING in Pisum sativum and discovery of natural sequence variations by Eco-TILLING in Arabidopsis thaliana.

CONCLUSION

We introduce a cost-effective tool based on a simplified purification protocol of a mismatch-specific and sensitive endonuclease, ENDO1. Especially, we report the successful applications of ENDO1 in mutation diagnostics in humans, fingerprinting of complex population of viruses, and in TILLING and Eco-TILLING in plants.

Compatibility counts: MHC-associated mate choice in a wild promiscuous primate

The mechanisms and temporal aspects of mate choice according to genetic constitution are still puzzling. Recent studies indicate that fitness is positively related to diversity in immune genes (MHC). Both sexes should therefore choose mates of high genetic quality and/or compatibility. However, studies addressing the role of MHC diversity in pre- and post-copulatory mate choice decisions in wild-living animals are few. We investigated the impact of MHC constitution and of neutral microsatellite variability on pre- and post-copulatory mate choice in both sexes in a wild population of a promiscuous primate, the grey mouse lemur (Microcebus murinus). There was no support for pre-copulatory male or female mate choice, but our data indicate post-copulatory mate choice that is associated with genetic constitution. Fathers had a higher number of MHC supertypes different from those of the mother than randomly assigned males. Fathers also had a higher amino acid distance to the females' MHC as well as a higher total number of MHC supertypes and a higher degree of microsatellite heterozygosity than randomly assigned males. Female cryptic choice may be the underlying mechanism that operates towards an optimization of the genetic constitution of offspring. This is the first study that provides support for the importance of the MHC constitution in post-copulatory mate choice in non-human primates.

Rapid polymerase chain reaction (PCR)-single-stranded conformational polymorphism (SSCP) screening method for the identification of Aspergillus section Nigri species by the detection of calmodulin nucleotide variations

Single-stranded conformational polymorphism (SSCP) analysis for genetic diversity studies has been widely applied to detect indirectly sequence differences up to a single base in amplified DNA fragments of the same length, representing an alternative to gene sequencing. In this study SSCP analysis was used to detect sequence variations contained in an about 180-bp region of the calmodulin gene in order to identify Aspergillus section Nigri species. The method described shows that fluorescence-based SSCP analysis by capillary electrophoresis is cheaper and faster than direct sequencing, and suitable for computer-assisted analyses allowing discrimination between the Aspergillus species belonging to the Nigri section: A. aculeatus, Aspergillus 'atypic uniseriate', A. brasiliensis, A. carbonarius, A. ellipticus, A. foetidus, A. heteromorphus, A. ibericus, A. japonicus, A. niger, and A. tubingensis.

Autosomal dominant hypoparathyroidism with severe hypomagnesemia and hypocalcemia, successfully treated with recombinant PTH and continuous subcutaneous magnesium infusion

Activating calcium sensor receptor (CaSR) mutations often present with hypocalcemia and hypomagnesemia. Severe hypocalcemia with this mutation has been reported but severe hypomagnesemia has not been well described.

AIM

To identify the cause of severe hypocalcemia and hypomagnesemia in a young child, and explore the efficacy of continuous subcutaneous magnesium therapy as a safer alternative to intravenous magnesium.

PATIENT

A 2-8/12 year-old female with severe hypocalcemia and hypomagnesemia of unknown etiology.

METHODS

Genetic analysis was performed on the proband and both parents. The proband was treated with human parathyroid hormone (teriparatide) and a continuous infusion of subcutaneous magnesium sulfate initially using a Deltec insulin pump and subsequently a Curlin infusion pump.

RESULTS

The patient has a known de novo mutation in the CASR gene (A843E). She could not be adequately managed with enteral and intravenous electrolyte replacement even after adding teriparatide. She responded well to adjunctive therapy with continuous subcutaneous magnesium.

CONCLUSIONS

Severe hypomagnesemia can be part of the phenotype of activating CaSR mutations. Subcutaneous magnesium should be considered in patients with difficult to control hypomagnesemia.

Identification of estrogen receptor alpha gene polymorphisms by SSCP and its effect on reproductive traits in Japanese flounder (Paralichthys olivaceus)

Estrogen receptor (ERalpha) modifies the expression of genes involved in cell growth, proliferation and differentiation through binding to estrogen response elements (EREs) located in a number of gene promoters, so the ERalpha gene is considered as an important factor affecting reproductive endocrinology in Japanese flounder (Paralichthys olivaceus). In this study, twelve single nucleotide polymorphisms (SNPs) within eight CDS exons and 1 kb of 3'-UTR of the ERalpha gene were tested to association with four reproductive traits in a population of 119 Japanese flounder individuals with polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP). The association analysis of SNPs within Japanese flounder ERalpha gene with the reproductive traits was carried out using General Linear Model (GLM) estimation. Results indicated that two SNPs in the exon4 of ERalpha gene, P1 (A803G and C864T), were significantly associated with hepatosomatic index (HSI) (P<0.05) in female Japanese flounder. Other ten SNPs in 3'-UTR associated to serum 17beta-estradiol (E(2)) and HSI showed that P2 (A1982T) was significantly associated with E(2) (P<0.01) and P3 (A2149G, 2181TTACAAG2182 insertion or deletion, T2324G, A2359G and G2391A) was significantly associated with HSI (P<0.05) in female Japanese flounder. However, P2 (A1982T) and P4 (G2256T, T2294C, T2309G and A2333T) had significant effects on E(2) (P<0.05 and P<0.01, respectively) in male Japanese flounder. In addition, there were significant associations between diplotype D1 based on fourteen SNPs and reproductive traits. The genetic effects for HSI (female) or E(2) (male) of diplotype D1 were significantly higher than those of other eight diplotypes (P<0.05), respectively. Our findings implied that P1 of ERalpha gene affecting the reproductive traits could be a potential QTN (quantitative trait nucleotide) which would be useful genetic marker in the selection of some reproductive traits for its in Japanese flounder.

Rapid differentiation of phenotypically similar yeast species by single-strand conformation polymorphism analysis of ribosomal DNA

Single-strand conformation polymorphism (SSCP) analysis of ribosomal DNA (rDNA) was investigated for rapid differentiation of phenotypically similar yeast species. Sensitive tests indicated that some yeast strains with one, most strains with two, and all strains with three or more nucleotide differences in the internal transcribed spacer 1 (ITS1) or ITS2 region could be distinguished by PCR SSCP analysis. The discriminative power of SSCP in yeast species differentiation was demonstrated by comparative studies of representative groups of yeast species from ascomycetes and basidiomycetes, including Saccharomyces species, medically important Candida species, and phylloplane basidiomycetous yeast species. Though the species within each group selected are closely related and have relatively similar rDNA sequences, they were clearly differentiated by PCR-SSCP analysis of the ITS1 region, given the amplified fragments were less than 350 bp in sizes. By using SSCP analysis for rapid screening of yeast strains with different rDNA sequences, species diversity existing in a large collection of yeast strains from natural sources was effectively and thoroughly investigated with substantially reduced time and cost in subsequent DNA sequencing.

Epigenetic and genetic analysis of the survivin promoter in acute myeloid leukemia

Survivin, an inhibitor of apoptosis (IAP) protein plays a dual role in regulation of mitosis and inhibition of apoptosis. Survivin is expressed in embryonic and fetal organs as well as in most human cancers, but not in normal differentiated adult tissues. In this study we investigated the molecular mechanism involved in overexpression of survivin in acute myeloid leukemia (AML). We used methylation specific PCR (MSP) and bisulfite sequencing to analyze the methylation status of the survivin promoter in primary AML samples and normal peripheral blood mononuclear cells (PBMCs). Both, in patients with de novo AML and normal control samples an unmethylated survivin promoter was present. Mutational analysis of the proximal survivin promoter revealed three single nucleotide polymorphisms (SNPs), where the frequently occurred polymorphism (G/C) at position -31 was detectable in both, AML blasts and healthy PBMCs and showed no significant impact on prognosis in de novo AML patients. These results suggest that the methylation status of the survivin promoter and occurrence of these SNPs within the promoter region of the survivin gene appear to be of minor importance in leukemogenesis.

Single-strand conformation polymorphism of microsatellite for rapid strain typing of Candida albicans

Single-strand conformation polymorphisms (SSCP) of Candida albicans' microsatellite CAI were characterized. Among the 76 clinical isolates recovered from different patients (independent strains), 60 distinct CAI SSCP patterns were recognized, resulting in a discriminatory power of 0.993. The multiple isolates recovered sequentially from the same or different body locations of the same patient showed exactly the same CAI SSCP pattern. The reliability of the SSCP analysis was confirmed by GeneScan and sequence analyses. From the same set of independent strains, 59 distinct CAI genotypes were identified by GeneScan analysis. Sequence comparison showed the advantage of SSCP over GeneSan analysis in the detection of point mutations in the microsatellite. The results indicated that PCR SSCP analysis of CAI microsatellite is a powerful and economical approach for rapid strain typing of C. albicans in clinical laboratories, especially in the detection of microevolutionary changes in microsatellites and in large-scale epidemiological investigation.

A novel β-myosin heavy chain gene mutation, p.Met531Arg, identified in isolated left ventricular non-compaction in humans, results in left ventricular hypertrophy that progresses to dilation in a mouse model

Mutations in the βMHC (β-myosin heavy chain), a sarcomeric protein are responsible for hypertrophic and dilated cardiomyopathy. However, the mechanisms whereby distinct mutations in the βMHC gene cause two kinds of cardiomyopathy are still unclear. In the present study we report a novel βMHC mutation found in a patient with isolated LVNC [LV (left ventricular) non-compaction] and the phenotype of a mouse mutant model carrying the same mutation. To find the mutation responsible, we searched for genomic mutations in 99 unrelated probands with dilated cardiomyopathy and five probands with isolated LVNC, and identified a p.Met531Arg mutation in βMHC in a 13-year-old girl with isolated LVNC. Next, we generated six lines of transgenic mice carrying a p.Met532Arg mutant αMHC gene, which was identical with the p.Met531Arg mutation in the human βMHC. Among these, two lines with strong expression of the mutant αMHC gene were chosen for further studies. Although they did not exhibit the features characteristic of LVNC, approx. 50% and 70% of transgenic mice in each line displayed LVH (LV hypertrophy) by 2–3 months of age. Furthermore, LVD (LV dilation) developed in approx. 25% of transgenic mice by 18 months of age, demonstrating biphasic changes in LV wall thickness. The present study supports the idea that common mechanisms may be involved in LVH and LVD. The novel mouse model generated can provide important information for the understanding of the pathological processes and aetiology of cardiac dilation in humans.

Angiotensinogen gene variants in a Pakistani hypertensive population of Punjab

Background. The renin-angiotensin-aldosterone system (RAAS) plays a key role in blood pressure (BP) regulation. Among the components of the RAAS, the gene for the angiotensinogen (AGT) has been extensively studied. Several studies in different populations link Threonine instead of methionine at position 235 (M235T) and Methinine instead of threonine at position 174 (T174M) polymorphisms with essential hypertension. We were unable to study these polymorphisms in the Punjab population of Pakistan through routine Restriction Fragment Length Polymorphism (RFLP) method. Considering the importance of this region we decided to further investigate the 300 bp region harbouring these two single nucleotide polymorphisms.

Methods. Samples were derived from a larger study group. Polymerase chain reaction amplified fragments were subjected to either RFLP or Single Strand Conformation. Polymorphism. Single stranded DNA showing mobility shift on denaturing gel were sequenced.

Results. Sequencing confirmed the presence of M235T and T174M polymorphisms in the local population. In addition to these polymorphisms one additional base was found at an identical position in two of the samples. We found a substitution of G with C just adjacent to T174M polymorphism in all seven of our samples studied.

Conclusions. We report two additional bases and one substitution in the angiotensinogen gene of Punjab population. We also suggest that SsmI can be used for the investigation of T174M polymorphism.

Cryptic lineages and hybridization in freshwater mussels of the genus Pyganodon (Unionidae) in northeastern North America

The distribution of freshwater mussels Pyganodon Crosse and P. Fischer, 1894 traditionally inferred from morphological characters was validated by a genetic characterization of the genus within the Quebec peninsula. Individuals were identified by comparing the sequences from the female mitochondrial genome (COI and 16S) with those of reference individuals, while hybridization was assessed with male mitochondrial (COI and COII) and nuclear genomes (ITS1 and ITS2). The results confirmed most of the previous morphological identifications but revealed unexpected results. Both male and female mitochondrial genomes support the distinction between Pyganodon fragilis (Lamarck, 1819) and Pyganodon cataracta (Say, 1817). However, only one lineage of Pyganodon grandis (Say, 1829), instead of the two expected, was detected in the sampled area. The genetic survey also revealed the presence of two unidentified Pyganodon lineages, previously unreported within the Quebec peninsula. These extremely rare lineages harbour the signature of ancestral hybridizations. Finally, recent divergence and hybridizations make shell characters only partially efficient in discriminating Pyganodon lineages.

Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation

The accurate analysis of genetic variation has major implications in many areas of biomedical research, including the identification of infectious agents (such as parasites), the diagnosis of infections, and the detection of unknown or known disease-causing mutations. Mutation scanning methods, including PCR-coupled single-strand conformation polymorphism (SSCP), have significant advantages over many other nucleic acid techniques for the accurate analysis of allelic and mutational sequence variation. The present protocol describes the SSCP method of analysis, including all steps from the small-scale isolation of genomic DNA and PCR amplification of target sequences, through to the gel-based separation of amplicons and scanning for mutations by SSCP (either by the analysis of radiolabeled amplicons in mutation detection enhancement (MDE) gels or by non-isotopic SSCP using precast GMA gels). The subsequent sequence analysis of polymorphic bands isolated from gels is also detailed. The SSCP protocol can readily detect point mutations for amplicon sizes of up to 450-500 bp, and usually takes 1-2 days to carry out. This user-friendly, low-cost, potentially high-throughput platform has demonstrated the utility to study a wide range of pathogens and diseases, and has the potential to be applied to any gene of any organism.