Use of proteinase K for RT-PCR of cytokine mRNA in formalin fixed tissue.

Fresh tissue from cases of sudden infant death syndrome is becoming increasingly scarce and therefore researchers interesting in studying the aetiology of this syndrome have had to resort to archival tissue, usually in the form of paraffin wax sections. A simple method for isolating mRNA from formalin fixed, paraffin wax embedded material of sufficient purity for reverse transcription (RT)-PCR is described. Proteinase K treatment of formalin fixed, wax embedded tissue followed by RNA STAT-60 extraction was successful in isolating mRNA suitable for RT-PCR. Interleukin (IL)-1alpha, IL-6 and tumour necrosis factor (TNF) transcripts were amplified successfully from heart, but not thyroid, kidney or liver tissue, of a patient who died following rejection of a transplanted heart, and IL-1alpha, but not IL-6 or TNF, transcripts from lung tissue of a six month old baby who died of viral pneumonia. Transcripts of a housekeeping gene were detected in all tissues. This method should be useful for examining gene expression in archival material.

Investigation of murine cytomegalovirus latency and reactivation in mice using viral mutants and the polymerase chain reaction.

Studies with 6 ts mutants of mouse cytomegalovirus indicated that mutants tsm1, tsm2, tsm3, and tsm6, like wild-type (wt) virus, produced acute infection in mice, became latent, and were reactivated as infectious virus immunosuppression. Using PCR, all five viruses expressed immediate-early (IE)-1, early (E)-1, and late (L, gB) genes during acute infection in all tissues examined (salivary glands, lung, spleen, liver, kidney, and heart). DNA was present in most tissues during latent infection with all five viruses, but transcription was restricted to the IE-1 gene in the salivary glands of wt infected mice only, suggesting true molecular latency rather than low level virus persistence. Similarly, mutant tsm5 expressed all three genes following primary inoculation. Although no detectable virus was produced, tsm5 subsequently entered the latent state as evidenced by DNA detection without RNA transcription indicating that productive infection is not required to initiate latency. This mutant also failed to reactivate from latency, although all three marker genes were expressed in most tissues. In contrast, tsm4 expressed all three marker genes and produced infectious virus during acute infection, then became latent. However, upon immunosuppression to reactivate tsm4, IE-1 and E-1 transcription occurred but neither gB transcription nor infectious virus was detectable in salivary glands, lung, spleen, liver, kidney, heart, or blood. The significance of this with regard to reactivation from latency is discussed.

Anti-epithelial (anti-A549) antibodies: their nature, specificity and relevance to transplantation.

Several studies have addressed the possible importance of anti-epithelial cell antibodies in kidney transplantation using the A549 cell line as an in vitro model. In this paper we report our results using for the first time an enzyme-linked immunosorbent assay (ELISA) to detect the anti-A549 cell antibodies. Sera from 129 kidney transplant patients were tested for IgM anti-epithelial cell antibodies directed against the A549 cell line prior to transplantation; only three sera were positive (2.3%). 101 of these patients were then followed-up post-transplantation; sera were collected routinely at 2, 6 and 12 weeks and at the time of rejection episodes. All samples were also tested for cytomegalovirus (CMV) IgM antibodies. Sixteen patients developed anti-A549 IgM antibodies, and there was no correlation with acute graft rejection. Anti-epithelial antibodies showed no binding to sections of normal kidney or biopsies of rejected kidneys. Eleven patients were positive for anti-CMV IgM antibodies. In nine cases both IgM anti-A549 and IgM anti-CMV antibodies were found, which was a highly significant association (p < 0.001). Analysis of A549 cellular proteins by immunoblotting gave evidence for the presence of CMV polypeptides in the cell lysate. Electron-microscopic examination of A549 cell preparations revealed intracellular particles which were compatible in size with CMV. Polymerase chain reaction analysis confirmed the presence of a specific CMV DNA sequence in A549 cells of several batches from different sources. Our data strongly suggest that the A549 cell line used in several published reports is infected with CMV and that in the majority of cases the anti-A549 'anti-epithelial' antibodies found in renal transplant patients are anti-CMV antibodies.

Fundamentals of the polymerase chain reaction: a future in clinical diagnostics?

The polymerase chain reaction (PCR) is an example of a technique that is having a profound impact on both fundamental and applied clinical science research. The availability of PCR-based diagnostic kits for the detection of polymorphisms within the HLA-DQA1 locus portends a technology that will undoubtedly become part of the clinical laboratory's diagnostic arsenal, and will extend and/or refine laboratory-based diagnosis in many areas. With current research effort directed to increase our knowledge of the overall structure of the human genome, and the identification of disease-associated genes and sequences, we can anticipate correspondingly rapid advances in its applications. This paper briefly reviews the basic facets of the PCR, which suggest it will fulfill such a role in future clinical diagnosis.

Sequencing of PCR-amplified DNA.

Alternatives for sequencing of PCR products essentially fall into one of two categories; generation of single-stranded DNA for sequencing or the direct sequencing of double-stranded product. Of the two alternatives, sequencing of double-stranded PCR products is likely to be of greatest immediate significance in terms of general applicability and rapidity. Double-stranded sequencing allows the use of the PCR product for other purposes either prior to or subsequent to generation of sequence data. The single-stranded sequencing methods generally require some prior decision regarding sequencing of the product. Assisted by automated workstation development, sequencing of single-stranded DNA PCR products generated either during thermal cycling or following affinity-capture strand separation may have significant future utility, particularly in genome mapping and routine clinical diagnosis. Despite template type and protocol differences, in all situations the purity and concentration of PCR-amplified DNA template used remains the most critical factor determining the efficiency and reliability of nucleotide sequencing methods.

Polymerase chain reaction for detection of human cytomegalovirus infection in a blood donor population.

We have used the polymerase chain reaction (PCR) to analyse 420 normal donor blood samples taken at a city centre donation site. Three sets of human cytomegalovirus (HCMV) primers specific to the HXLF6, immediate early and late antigen gp64 genes, of the alpha, beta and gamma antigen coding regions respectively, were used to allow for the possibility of sequence variation. There was perfect correlation between the three sets of primers. Latex agglutination and enzyme-linked immunosorbent assay (ELISA) were also employed to provide data for a comparative study. The complete data show that infection with human cytomegalovirus is not only age related but is also sex related. The female population examined using PCR reached a peak infection rate of 80% by the age of 40-50 years whereas the male population reached a 98% infection rate following an almost linear increase with age. Latex agglutination data shows a similar picture although the infection rate peaks around 20% lower than with PCR. The data shows an increase in sensitivity using the PCR rather than the serology although the clinical significance of this has yet to be determined. The work presented here also demonstrates the suitability of the polymerase chain reaction as a potential diagnostic and epidemiological tool.

Detection of Epstein-Barr virus antigens and DNA in major and minor salivary glands using immunocytochemistry and polymerase chain reaction: possible relationship with Sjogren's syndrome.

This study has investigated the presence of Epstein-Barr virus (EBV) in parotid (n = 12), submandibular (n = 15), and minor salivary glands (n = 25) using immunohistochemical methods for detection of EBV-encoded antigens and the polymerase chain reaction (PCR) for detection of viral DNA. Major salivary glands were from patients without connective tissue disease. Labial glands were from patients with primary Sjogren's syndrome (n = 10), rheumatoid arthritis (n = 8), or from normal individuals (n = 7). None of the glands exhibited specific reactivity for lytic (EA-D, EA-R, VCA) or latent (EBNA-2, LMP) viral antigens. Antibodies to EA-D, when used at 20-50 times their optimal concentration, gave lumenal staining of ducts and acini of all the specimens tested (n = 14), irrespective of the presence (n = 8) or absence (n = 6) of EBV-DNA by PCR. Ductal immunoreactivity for the EBV/C3d (CR2, CD21) receptor was found in 40 per cent of specimens. PCR detected EBV-DNA in 64 per cent submandibular, 46 per cent parotid, and 80 per cent of minor glands. There were no significant differences in the detection of EBV-DNA between specimen/patient groups. Only type A EBV was detected by strain typing PCR. These results indicate that EBV (type A), undetected immunocytochemically, is commonly present at low copy numbers within salivary glands irrespective of a clinical diagnosis of Sjogren's syndrome.

Analysis of human papillomavirus type 16 E6-E7 transcription in cervical carcinomas and normal cervical epithelium using the polymerase chain reaction.

Cervical biopsies were collected from Birmingham women having cervical intraepithelial neoplasia or invasive cervical carcinoma and normal controls, and examined for the presence of human papillomavirus type 16 (HPV-16) E6-E7 DNA and mRNA using an adaptation of the polymerase chain reaction. HPV-16 E6-E7 sequences were detected in all abnormal biopsies and in 90% of the normal biopsies examined, confirming previous studies describing the high prevalence of cervical HPV-16 infection. While we were unable to identify any qualitative differences in RNA transcripts from the p97 promoter, substantial quantitative differences in HPV-16-specific early region transcripts between normal and cytologically abnormal cervices were observed. These results suggest that although the level of E6-E7 transcription may contribute to the malignant phenotype, additional factors are likely to be important in the development of cervical neoplasia.

Synthesis in vitro and application of biotinylated DNA probes for human papilloma virus type 16 by utilizing the polymerase chain reaction.

The polymerase chain reaction (PCR) has been used to incorporate biotinylated deoxynucleotide triphosphate analogues into a 120 bp sequence from the E6 region of human papilloma virus type 16 (HPV 16). No loss of amplification efficiency is observed utilizing concentrations of up to 200 microM-biotin-11-dUTP, or 180 microM-biotin-7-dATP and -biotin-16-dUTP (where the numbers refer to the number of carbon atoms in the spacer arms). Internally biotinylated PCR products can be detected following slot-blot or vacuum transfer to mitrocellulose or nylon filters without prior electrophoretic separation of the reactants, since unincorporated biotinylated analogues pass through the filter. Internally biotinylated PCR products can also be applied as hybridization probes in Southern blot analysis or in situ hybridization. This system enables detection of PCR products or target sequences at levels below that for 5'-biotinylated probes and can be applied in an 'open sandwich assay' without the need for a separate labelled probe currently required in conventional sandwich assays. However, as hybridization probes, sensitivity may be limited by the steric hindrance of strand hybridization possibly due to the spacer arms linking the nucleotides to the biotin molecule.

Detection of HPV 6 and 11 in tumours of the upper respiratory tract using the polymerase chain reaction.

We have applied the polymerase chain-reaction (PCR) technique to benign and malignant squamous tumours of the pharynx and larynx and to nasal inverted papillomas to detect evidence of infection with human papillomavirus (HPV) 6 and 11. Each of these lesions tended to be infected with either or both of these but the prevalence of infection when compared with that of histologically normal biopsies from the nasopharynx was not significantly increased.

Demonstration of Epstein-Barr virus in primary brain lymphoma by in situ DNA hybridisation in paraffin wax embedded tissue.

Tumour tissue from 29 patients with primary brain lymphoma was reviewed to determine if there was an aetiological association between Epstein-Barr virus and polyclonal and monoclonal lymphoproliferations. The morphology and immunophenotype in 24 patients for whom paraffin wax embedded tissue was available were studied. A high grade pleomorphic tumour morphology with plasmacytoid features was seen in 13 tumours. Because of the large number of pleomorphic lymphomas, all tumours were examined for the presence of the Epstein-Barr virus genome using in situ DNA hybridisation. A panel of three biotinylated probes to different sequences in the Epstein-Barr virus genome was used. Positive hybridisation with one or more probes was shown in tumours from 11 patients. The remaining tumours gave no hybridisation signal. There was no correlation between positive hybridisation and morphological subtype or clinical outcome.

Demonstration of multiple HPV types in normal cervix and in cervical squamous cell carcinoma using the polymerase chain reaction on paraffin wax embedded material.

The prevalence of human papilloma virus (HPV) types 6, 11, 16 and 18 was investigated using the polymerase chain reaction on formalin fixed, paraffin wax embedded material in 19 cases of cervical squamous cell carcinoma and in 10 normal cervices. HPV DNA was detected in 16 of 19 carcinomas, with multiple types present in 11 of these. HPV 16 or 18, or both, were present in all cases in which HPV was shown. Six of 10 cases of normal cervix contained HPV; five of these contained two or more HPV types, including HPV 16 or 18, or both. This study shows the feasibility of using the PCR on paraffin wax embedded material and indicates a high rate of carriage of multiple HPV types in both normal and neoplastic cervix.

The polymerase chain reaction: a new epidemiological tool for investigating cervical human papillomavirus infection.

The polymerase chain reaction is an in vitro method for primer directed enzymatic amplification of specific target DNA sequences. The technique was used to detect human papillomavirus types 11 and 16 simultaneously in cellular DNA recovered from cervical smears in 38 women referred for colposcopy to evaluate cytological abnormality and 10 women with no history of cytological abnormality. The polymerase chain reaction was shown to be both specific and sensitive in detecting human papillomavirus DNA such that a single human papillomavirus molecule was detected in 10(5) cells. Of the 38 women with cytological abnormality, all were positive for human papillomavirus on testing with the polymerase chain reaction; 36 were infected with human papillomavirus type 16 and 22 dually infected with human papillomavirus types 11 and 16. Seven of the 10 women with no cytological abnormality were also infected with human papillomavirus type 11 or 16. The use of the polymerase chain reaction will facilitate epidemiological investigation of the aetiological role of human papillomavirus in cervical neoplasia. This preliminary analysis suggests that the prevalence of human papillomavirus infection is greater than previously reported.