CpG-island methylation study of liver fluke-related cholangiocarcinoma

BACKGROUND

Genetic changes have been widely reported in association with cholangiocarcinoma (CCA), while epigenetic changes are poorly characterised. We aimed to further evaluate CpG-island hypermethylation in CCA at candidate loci, which may have potential as diagnostic or prognostic biomarkers.

METHODS

We analysed methylation of 26 CpG-islands in 102 liver fluke related-CCA and 29 adjacent normal samples using methylation-specific PCR (MSP). Methylation of interest loci was confirmed using pyrosequencing and/or combined bisulfite restriction analysis, and protein expression by immunohistochemistry.

RESULTS

A number of CpG-islands (OPCML, SFRP1, HIC1, PTEN and DcR1) showed frequency of hypermethylation in >28% of CCA, but not adjacent normal tissues. The results showed that 91% of CCA were methylated in at least one CpG-island. The OPCML was the most frequently methylated locus (72.5%) and was more frequently methylated in less differentiated CCA. Patients with methylated DcR1 had significantly longer overall survival (Median; 41.7 vs 21.7 weeks, P=0.027). Low-protein expression was found in >70% of CCA with methylation of OPCML or DcR1.

CONCLUSION

Aberrant hypermethylation of certain loci is a common event in liver fluke-related CCA and may potentially contribute to cholangiocarcinogenesis. The OPCML and DcR1 might serve as methylation biomarkers in CCA that can be readily examined by MSP.

p53 status and human papillomavirus infection in Thai women with cervical carcinoma

Loss of p53 function has been implicated in a wide variety of human malignacies. Many studies suggest that in cervical carcinoma p53 function is inactivated either by gene mutation or by complex formation with E6 oncoprotein product of high-risk human papillomavirus (HPV). The aim of this study was to determine the status of HPV infection and p53 gene mutation as well as their correlation in cervical carcinomas. Formalin-fixed paraffin-embedded tissues of 12 cervicitis, 21 cervical intraepithelial neoplasia grade 3 (CIN 3) and 17 squamous cell carcinomas were determined for the presence of HPV using polymerase chain reaction (PCR) amplification and dot blot hybridization. The status of p53 mutations in exons 5-8 was evaluated by polymerase chain reaction single strand conformation polymorphism (PCR-SSCP) and confirmed by direct nucleotide sequencing. HPV infections were detected in all CIN 3 and squamous cell carcinomas (100%). Mutations of p53 were present in 3 of 38 HPV-positive samples: one with an ATG-->TTG transversion (Met-->Leu) in codon 237 of exon 7; and the others with a TGC-->TGG transversion (Cys-->Trp) in codon 242 of exon 7, and a CGT-->CCT transversion (Arg-->Pro) in codon 273 of exon 8, respectively. Our findings show that the frequency of p53 mutation is low in primary cervical carcinoma and that the p53 gene mutation and HPV infection are not mutually exclusive events in the development of cervical cancer. Thus, other genetic events independent of p53 inactivation may also significantly contribute to the carcinogenesis of the uterine cervix.

Production and evaluation of Taq DNA polymerase

Taq DNA polymerase is an enzyme essential in performing Polymerase Chain Reaction (PCR) which has recently become a basic technology in research and diagnostic laboratories. In order to reduce the cost of research work in Thailand, recombinant Taq DNA polymerase was locally produced from pTaq cloned in E. coli. The enzyme was characterized and evaluated in comparison with the commercial Taq DNA polymerase produced by Perkin Elmer Cetus, U.S.A. The yield of enzyme was 6.72 mg/ml and the activity of 9,524 units/mg protein with the total of 448,000 units/litre of the bacterial culture. The preparation was free of DNase based upon its ability to degrade Lambda DNA evaluated by gel electrophoresis. Although the enzyme produced gave a high DNA polymerase activity, the preparation was not as pure as the enzyme produced by Perkin Elmer Cetus. Immunoblot analysis indicated that the enzyme preparation contained the products of enzyme degradation obtained during preparation and bacterial protein contaminations. In spite of the existence of bacterial proteins in the preparation, the Taq enzyme produced was proved to be applicable in performing PCR such as the PCR-SSP (Sequence Specific Primers) typing for HLA-DR. The cost of enzyme preparation was about 256 times less than that of the commercial enzyme. Economically, the locally produced Taq DNA polymerase can be used efficiently in the research laboratories performing PCR based typing of the HLA genes.

Nucleotide sequence of the first cosmid from the Mycobacterium leprae genome project: structure and function of the Rif-Str regions

The nucleotide sequence of cosmid B1790, carrying the Rif-Str regions of the Mycobacterium leprae chromosome, has been determined. Twelve open reading frames were identified in the 36716bp sequence, representing 40% of the coding capacity. Five ribosomal proteins, two elongation factors and the beta and beta' subunits of RNA polymerase have been characterized and two novel genes were found. One of these encodes a member of the so-called ABC family of ATP-binding proteins while the other appears to encode an enzyme involved in repairing genomic lesions caused by free radicals. This finding may well be significant as M. leprae, an intracellular pathogen, lives within macrophages.

The 42-kilodalton rhoptry-associated protein of Plasmodium falciparum

The gene coding for a 42-kDa rhoptry protein of Plasmodium falciparum has been cloned. On the basis of prior monkey vaccination studies, this protein is regarded as an important vaccine candidate, but its identity has been the subject of considerable uncertainty. Analysis of the cloned sequence shows that it is a basic, hydrophobic protein, without repetitive elements, unrelated to any of the previously postulated gene products and shows minimal sequence diversity. The availability of the corresponding recombinant protein will enable studies of its efficacy in human vaccine trials to be undertaken.

7H8/6, a multicopy DNA probe for distinguishing isolates of Plasmodium falciparum

A method using DNA fingerprinting to distinguish Plasmodium falciparum isolates has been developed using a clone, 7H8/6, isolated by screening a genomic expression library of the Malayan Camp strain with a monoclonal antibody. Unlike other P. falciparum DNA probes that contain internally repetitive sequences, this probe contains a single full-length open reading frame and lacks any repetitive sequences. Chromosome mapping located the hybridizing sequences to most chromosomes. 7H8/6 sequences are located at sites near the subtelomeric regions, although they are further from the telomeres than the subtelomeric repetitive sequences rep20. The probe gave multiple polymorphic bands on Southern blots of genomic DNA allowing all unrelated isolates tested to be readily distinguished. Hybridization patterns of parent and progeny from the genetic cross of two P. falciparum clones showed that most bands were inherited independently and no new bands were generated during the cross. This probe is useful for distinguishing isolates of P. falciparum and also for analyzing relationships between closely related isolates.

Characterization of a Plasmodium falciparum epitope recognized by a monoclonal antibody with broad isolate and species specificity

Monoclonal antibody (MAb) 7H8 raised against Plasmodium yoelii reacted with a series of proteins from P. falciparum that range in molecular weight from 46 to 194 kDa. By immunofluorescence assay, this MAb reacted with all isolates of P. falciparum tested. MAb 7H8 was used to screen a genomic expression library of asexual blood stage antigens of P. falciparum, Malayan Camp K+ and 7 independent clones were identified. These 7 clones were sequenced and the epitope recognized by MAb 7H8 in the recombinant protein of one of these clones was mapped. This epitope contained Lys Tyr Pro as core amino acids. However, similar sequences were not found in the other clones, indicating that this MAb binds to a structural epitope formed by different amino acids. The variable composition of the epitope may account for the number of P. falciparum malarial proteins recognized by MAb 7H8.

The relationship of phosphorylation of membrane proteins with the osmotic fragility and filterability of Plasmodium berghei-infected mouse erythrocytes

Membrane from Plasmodium berghei-infected mouse erythrocytes showed a pattern of protein phosphorylation which was substantially altered from the normal pattern, with an increase in the phosphorylation of the protein with an apparent molecular weight of 43,000 (M 43), which increased from undetectable in uninfected cells to a maximum in the mature trophozoite stage. Phosphorylation levels of this and other minor bands were strongly correlated with osmotic fragility and filterability. The level of M 43 phosphorylation in membranes from cells which remained intact in a hypotonic medium was 3.82 +/- 0.59-times that of lysed cells, compared with the value of 0.76 +/- 0.07 calculated from distribution alone. Results found when intact erythrocytes were phosphorylated by incubation with [32P]Pi prior to partial lysis were similar to those found when membranes from the lysed and unlysed fractions were subsequently phosphorylated with [gamma-32P]ATP. Infected erythrocytes which could pass repeatedly through 3-micron polycarbonate filters had a much higher phosphorylation level for the M 43 region than whole infected cells with similar parasitemia and stage distribution. The phosphorylation change could play a role in the control of osmotic and mechanical properties of the infected erythrocytes during maturation.