Molecular diagnosis : a journal devoted to the understanding of human disease through the clinical application of molecular biology最新文献

Background: Gene promoter methylation is a mechanism for tumor suppressor gene silencing and inactivation. The development of highly sensitive methods for revealing aberrant cancer-associated DNA methylation allows the identification of tumor markers not only in tumor samples, but also in body fluid, an approach that can be useful in the early detection of neoplasms.

Methods: We analyzed the methylation status at 16 loci in tumor samples of the gastrointestinal tract and in early or pre-neoplastic lesions of the colon.

Results: Tumor samples revealed that methylation at the transmembrane protein containing epidermal growth factor and follistatin domains (TPEF) locus had the best ratio of discrimination between tumor samples versus normal tissues (83 versus 0%). Its combination with hypermethylated in cancer 1 (HIC1), death-associated protein kinase (DAPK) and O-6-methylguanine DNA methyltransferase (MGMT), allowed the detection of aberrant methylation in 98% of colorectal carcinomas and 100% of gastric carcinomas. The same alterations were also detected in colon adenomas and tissues surrounding the adenomas, indicating that hypermethylation at these loci occurred early in tumor progression. Analysis of DNA from peripheral blood revealed that TPEF methylation was detectable in colorectal tumor patients and patients with early or pre-neoplastic lesions, but not in healthy volunteers.

Conclusions: Our results identify TPEF as a tumor marker that could be useful in the follow-up of gastrointestinal cancer patients or the screening of individuals at risk of developing gastrointestinal neoplasms.

Background: Nuclear factor-kappa B (NF-kappa B) is an important transcription factor involved in the regulation of immune responses as well as in cell proliferation and survival. An abnormal and constitutive activation of NF-kappa B is observed in many pathological states as diverse as inflammation, neurological diseases, and cancer.

Methods and results: Termination of NF-kappa B transcription is mediated through the NF-kappa B-dependent synthesis of the I kappa B-alpha inhibitory subunit. To quantify NF-kappa B activation we measured by real-time PCR the expression of I kappa B-alpha mRNA. The PCR data perfectly matched the results obtained by Northern blot or gene reporter analysis when Jurkat leukemic T cells or HeLa carcinoma cells were stimulated with various activators of NF-kappa B, such as the cytokine tumor necrosis factor (TNF)-alpha or the phorbol ester PMA. Constitutive NF-kappa B activation in Hodgkin's lymphoma cell line could also be evaluated by this approach. Kinetic experiments in HeLa cells show that TNF stimulation first induced NF-kappa B DNA binding within 30 minutes, followed by I kappa B-alpha gene transcription 30 minutes later. Removal of TNF after stimulation resulted in a faster decrease in both NF-kappa B DNA binding activity and I kappa B-alpha mRNA levels. No accumulation or stabilization of I kappa B-alpha mRNA was detected that could bias interpretation of the results. The sensitivity of the method allowed the detection of NF-kappa B activation in stimulated normal peripheral blood lymphocytes.

Conclusion: The real-time PCR measure of I kappa B-alpha mRNA levels is a rapid, sensitive, and powerful method to quantify the transcriptional power of NF-kappa B. It can be easily used for clinical evaluation of NF-kappa B status.

Background: Lyme disease is a multisystem, multistage infection caused by three genospecies of the Borrelia burgdorferi sensu lato species. The diagnosis of Lyme disease is based on a history of tick-bite, physical examination, and serological tests. In the seronegative patients with Lyme borreliosis symptoms, additional testing should be introduced.

Methods: The study group was composed of 240 hospitalized patients presented with various clinical symptoms suggesting Lyme borreliosis: 221 of the patients with neurological abnormalities and 19 with oligoarticular arthritis. Citrated blood and serum samples were collected from the patients for culture and serological examination, respectively. Moreover, 173 cerebrospinal and 6 synovial fluid samples were tested. New oligonucleotide primers based on B. burgdorferi sensu lato 16SrRNA gene sequences were designed for the detection of the bacteria in blood, cerebrospinal, and synovial fluid specimens with PCR. Levels of specific antibodies were measured in serum, cerebrospinal fluid and synovial fluid samples using ELISA and Western blot. B. burgdorferi spirochetes from blood, cerebrospinal fluid, and synovial fluid samples were cultured in cell line. Extracted and purified B. burgdorferi DNA was identified by PCR with new oligonucleotide primers. Then three genospecies were identified by PCR amplification with other primer sets specific for 16S rDNA and/or by the restriction fragment length polymorphism of 23S(rrl)-5S(rrf).

Results: Bacterial DNA were found in samples from 32 patients, including 28 patients with neuroborreliosis and 4 with Lyme arthritis. B. burgdorferi-specific IgM and/or IgG serum antibodies were detected in 14 of these patients. Fourteen strains of Borrelia garini, 4 strains of Borrelia afzelii and 1 strain of B. burgdorferi sensu stricto were identified by PCR. Genospecies were not recognized in 13 specimens.

Conclusions: The procedure can be a rapid and sensitive diagnostic method for the detection of etiological agents in clinical materials derived from patients with the clinical symptoms of Lyme borreliosis. It can be utilized for both basic research as well as routine laboratory diagnosis.

Background: Our understanding of fragile X syndrome can be improved by reversing the expression of the silenced fragile X mental retardation 1 (FMR1) gene in immortalized cells from these patients. Epstein-Barr virus (EBV) infection has been extensively used to transform B cells into a permanent lymphoblastoid cell line.

Methods: We immortalized B lymphocytes from three different fragile X patients and one normal male. We analyzed the CGG triplet repeats and methylation status of the FMR1 and interferon (IFN)-gamma promoter. We also assayed FMR1 mRNA levels by real-time PCR and FMR1 protein (FMRP) by Western blot.

Results: We observed that EBV transformation may induce the instability of CGG repeats and DNA demethylation that can lead to the modification of mRNA expression.

Conclusions: EBV transformation may induce variable changes in the genome that can lead to the misinterpretations of experimental data obtained from these cells. Thus, periodic testing of DNA from immortalized cells should be routinely undertaken to detect undesired effects.

Background: We report on a novel mutation (S270T) in the M2 domain of the GLRA1 (alpha subunit of the glycine receptor) gene causing autosomal dominant hyperekplexia in a neonate, the mother and maternal uncle. All affected members showed the typical clinical features of the disorder. This novel S270T (T1188A) mutation is located in the boundary of the transmembrane M2 domain of the GLRA1 protein, close to other previously reported mutations. Mutations in this 'hot spot' domain of GLRA1 are frequent in autosomal dominant hyperekplexia but are not usually seen in the autosomal recessive form of the disease in which both the M1 and the carboxy terminal domains have been implicated.

Methods: Genomic DNA was extracted by standard procedures from peripheral blood leukocytes and exon 6 of the GLRA1 gene was amplified using primers and PCR conditions. A complete sequence analysis of the fragment was performed. DNA sequences were analyzed both by direct observation of the electropherogram and by comparison with the published sequence.

Results: The proband had metabolic acidosis, which was probably related to continuous contractions of somatic muscles and intractable hypertonia. Data seem to show a direct relationship between the mechanism of inheritance of the disorder and the location of the molecular defect. The patients showed almost all the clinical signs of hyperekplexia: exaggerated startle response, muscle hypertonia in response to unexpected tactile and/or auditory stimuli, hyperexcitability, and sudden falls.

Maturity onset diabetes of the young (MODY) is caused by mutations in at least six different genes, including the glucokinase gene (MODY 2) and genes encoding the tissue-specific transcription factors (MODY 1 and MODY 3-6). To determine the presence of mutations in MODY 2 in four members of a family who have the clinical characteristics of MODY, we performed polymerase chain reaction and single strand conformation polymorphism screening, followed by DNA sequencing. We found a novel mutation which consisted of the deletion of a cytosine in the position 2 of the exon 5 codon 168. This mutation produced a frame shift which determines a stop codon at position 203 in exon 6. The identification of a mutation in glucokinase gene and transcription factor genes in patients with early-onset diabetes confirms the diagnosis of MODY and has important implications for clinical management.

Aim: DNA testing can provide a definitive diagnosis of familial hypercholesterolemia (FH), even in the absence of the clinical characteristics of this inherited cardiovascular disease (CVD) subtype. Our aim was to design a rapid diagnostic assay capable of simultaneously analyzing seven point mutations in the low-density lipoprotein receptor (LDLR) gene, which occur at high frequency in South African FH patients.

Methods: The test is based on multiplex DNA amplification and hybridization to membrane strips presenting a parallel array of immobilized allele-specific oligonucleotide probes.

Results: A reverse-hybridization assay for genotyping LDLR point mutations D154N, D200G, D206E, C356Y, G361V, V408M, and P664L was set-up and validated using pretyped human DNA samples, as well as recombinant plasmid clones containing mutant alleles. The procedure is rapid (6 hours) and may be automated to a large extent.

Conclusions: The new FH strip-assay forms an important part of the comprehensive cardiovascular genetic screen offered routinely to high-risk population groups in South Africa. A genetic approach based on FH testing in conjunction with other 'genetic' CVD risk factors is feasible and justified, since the spectrum of disease-related mutations have been defined to a large extent in the genetically distinct population groups of South Africa. Knowledge of a significantly increased CVD risk due to the presence of gene variations, which can be targeted for risk reduction by the avoidance of relevant environmental risk factors and the appropriate treatment, provides a powerful message to motivate people into implementing preventative measures based on their genetic profile.

Background: In recent years PCR has proven to be a highly sensitive and specific method for the diagnosis of infections caused by Neisseria meningitidis.

Study design: We developed and evaluated a N. meningitidis LightCycler real-time duplex PCR (NM-LCdPCR) capable of simultaneously detecting and distinguishing between two separate genes on the N. meningitidis genome.

Methods: The NM-LCdPCR was developed on the LightCycler platform (Roche Diagnostics, Castle Hill, NSW, Australia) and comprised two primer pairs and two hybridization probe sets, enabling the detection of both the porA and ctrA genes within the same reaction mix. To distinguish between the fluorescence emitted by each hybridization probe set, each downstream probe was labeled with a different fluorophore (either LC-Red640 or LC-Red705). The results obtained by the NM-LCdPCR were then compared with the results obtained by a mono-specific LightCycler assay targeting the porA gene only (porA-LCPCR).

Patients: One-hundred and forty-eight clinical samples from patients with suspected meningococcal infection were evaluated.

Results: The results of the NM-LCdPCR and porA-LCPCR gave 100% agreement; N. meningitidis DNA was detected in 25 samples whereas 123 samples were negative by both assays. The breakdown of the NM-LCdPCR results show that both genes were detected in 26 of the 28 positive samples.

Discussion: By targeting two separate N. meningitidis genes, the NM-LCdPCR has the potential to prevent the false-positive results which may arise from sequence variation. In addition, the ability to detect and discriminate between the two different N. meningitidis genes within the same reaction mix offers a rapid means for confirming the presence of N. meningitidis DNA in clinical samples, thereby reducing the need for subsequent confirmatory assays to be performed.

Conclusions: The sensitivity and specificity of the NM-LCdPCR assay, combined with its ability to detect and discriminate both the N. meningitidis porA and ctrA genes, make it suitable for the diagnosis of N. meningitidis infections in the routine clinical laboratory.