In-situ polymerase chain reaction

Diagnostic Implication and Clinical Relevance of Ancillary Techniques in Clinical Pathology Practice

Hematoxylin–eosin-stained slide preparation is one of the most durable techniques in medicine history, which has remained unchanged since implemented. It allows an accurate microscopic diagnosis of the vast majority of tissue samples. In many circumstances, this technique cannot answer all the questions posed at the initial diagnostic level. The pathologist has always been looking for additional ancillary techniques to answer pending questions. In our daily histopathology practice, we referred to those techniques as special stains, but nowadays, they are more than stains and are collectively called ancillary tests. They include a wide range of techniques starting from histochemical stains and ending in one or more advanced techniques, such as immunohistochemistry, immunofluorescence, molecular studies, cytogenetic studies, electron microscopy, flow cytometry, and polymerase chain reaction.

Human Immunodeficiency Virus Localization in Human Papillomavirus-Related, High-Grade Squamous Intraepithelial Lesions of the Cervix in Women with HIV Infection: Microdissection and Molecular Analysis on Formalin-Fixed and Paraffin-Embedded Specimens

OBJECTIVES

To evaluate a possible mechanism of human immunodeficiency virus (HIV) and human papillomavirus (HPV) interaction, we have identified the cervical tissue compartments that harbor HIV.

MATERIALS AND METHODS

We studied 39 paraffin-embedded, cervical conization specimens with high-grade cervical intraepithelial neoplasia (CIN3) occurring in HIV-infected women. From selected intraepithelial HPV-positive nonulcerated specimens (confirmed by in situ hybridization), we obtained serial 4- to 5-μm-thick sections that were stained with hematoxylin and eosin, anti-S100 protein, and anti-CD4. The presence of intramucosal Langerhans' cells or dendritic cells or CD4-positive cells was recorded. Three consecutive, nonmicrodissected, full-thickness sections of the same specimens were used for polymerase chain reaction (PCR) analysis (group A). Three other uncovered, consecutive sections from the same blocks were examined with an inverted microscope, and full-thickness specimens of mucosa were dissected from the underlying cervical stroma, were gently removed, and were used for PCR (group B). The quality of DNA was checked by HLA-DQa amplification; then a nested PCR for HIV proviral DNA was performed.

RESULTS

Of group A, 5 of 39 cases (12.8%) were positive, whereas HIV was not detected in the microdissected sections of group B, with or without intraepithelial Langerhans' or CD4 cells.

CONCLUSIONS

HIV does not affect cervical epithelium. The absence of infected Langerhans' or dendritic cells (or both) indicates a migration to the proximal lymph nodes of the in ….

Direct in situ rt-PCR

In situ polymerase chain reaction (PCR) is a histological technique that exploits the advantages of PCR for detection of mRNA directly in tissue sections. It somehow conjugates together PCR and in situ hybridization that is more traditionally employed for mRNA localization in cell organelles, intact cells, or tissue sections. This chapter describes the application of in situ PCR for neuropeptide mRNA localization. We provide here a detailed protocol for direct in situ reverse transcription (RT) PCR (RT-PCR) with nonradioactive probes after fixation and paraffin embedding or cryosectioning. Digoxigenin-labeled nucleotides (digoxigenin-11-dUTP) are incorporated in the PCR product after RT and subsequently detected with an anti-digoxigenin antibody conjugated with alkaline phosphatase. The procedure can be modified for use with fluorescent probes and employed in combination with enzyme/fluorescence immunocytochemical labeling.

In situ detection of antibiotic-resistance elements in single Bacillus cereus spores

Rapid detection of Bacillus spores is a challenging task in food and defense industries. In situ labeling of spores would be advantageous for detection by automated systems based on single-cell analysis. Determination of antibiotic-resistance genes in bacterial spores using in situ labeling has never been developed. Most of the in situ detection schemes employ techniques such as fluorescence in situ hybridization (FISH) that target the naturally amplified ribosomal RNA (rRNA). However, the majority of antibiotic-resistance genes has a plasmidic or chromosomal origin and is present in low copy numbers in the cell. The main challenge in the development of low-target in situ detection in spores is the permeabilization procedure and the signal amplification required for detection. This study presents permeabilization and in situ signal amplification protocols, using Bacillus cereus spores as a model, in order to detect antibiotic-resistance genes. The permeabilization protocol was designed based on the different layers of the Bacillus spore. Catalyzed reporter deposition (CARD)-FISH and in situ polymerase chain reaction (PCR) were used as signal amplification techniques. B. cereus was transformed with the high copy number pC194 and low copy number pMTL500Eres plasmids in order to induce resistance to chloramphenicol and erythromycin, respectively. In addition, a rifampicin-resistant B. cereus strain, conferred by a single-nucleotide polymorphism (SNP) in the chromosome, was used. Using CARD-FISH, only the high copy number plasmid pC194 was detected. On the other hand, in situ PCR gave positive results in all tested instances. This study demonstrated that it was feasible to detect antibiotic-resistance genes in Bacillus spores using in situ techniques. In addition, in situ PCR has been shown to be more sensitive and more applicable than CARD-FISH in detecting low copy targets.

Diagnostic value of in situ Polymerase Chain Reaction in leprosy

OBJECTIVE

This prospective study was carried out to assess the diagnostic value of in situ Polymerase Chain Reaction in leprosy, particularly in enhancing the histopathological diagnosis.

METHOD

Clinical examination of 20 patients (< 16 yr) was done and skin smear for AFB was prepared. Biopsy of lesion site was taken for histopathological examination and in situ PCR testing.

RESULTS

The histopathological examination confirmed the clinical diagnosis in 45% cases only; non-specific histopathology was reported in the remaining 55% cases. In situ PCR showed a positivity of 57.1% in early/localized form of leprosy (IIBT) and 61.5% in (BB/BL) group. When compared to histopathology examination, a significant enhancement of 15% in diagnosis was seen. With in situ PCR, the diagnosis could be confirmed in 4/11 (36.3%) cases with non-specific histopathological features, (which is common in early disease) in addition to confirmation of 8/9 (88.8%) histopathologically-confirmed tissue sections. Histopathology and in situ PCR, combined together, confirmed the diagnosis in 13/20 cases (65% of total cases).

CONCLUSION

Thus, in situ PCR is an important diagnostic tool especially in early and doubtful cases of leprosy.

Detection of human immunodeficiency virus type 1 RNA by in situ hybridization in oral mucosa epithelial cells from anti-HIV-1 positive patients

Several in vitro studies have shown that HIV-1 can infect CD4 negative epithelial cells of different origin including normal human oral keratinocytes, but whether this infection of mucosal epithelial cells occurs in vivo is still unclear. In this report, the presence and cell types infected by HIV-1 in paraffin embedded oral mucosa biopsies from 17 anti-HIV-1 positive patients have been examined by in situ hybridization and immunohistochemistry. As controls, oral mucosa biopsies from eight patients without HIV-1 infection markers were also analyzed. The results showed that 8 out of the 17 anti-HIV-1 positive patients had HIV-1 RNA detectable in plasma. Positive hybridization signals were observed in the mucosa biopsies from 14 of the 17 anti-HIV-1 patients (82.3%). The mean percentage of cells showing HIV-1 RNA was 2.64% +/- 1.77% (range: 1% to 5.5%). No differences in the mean percentage of HIV-1 infected cells were found between patients with and without HIV-1 RNA in plasma (3.01% +/- 1.57% vs. 3.4% +/- 1.27% respectively), or between untreated patients and patients under antiretroviral therapy (2.83% +/- 1.63% vs. 3.42% +/- 1.29% respectively). Immunohistochemical detection of S-100 antigen, cytokeratin and CD4 showed that hybridization signals appeared in cytokeratin positive cells and CD4 positive cells but not in S-100 positive cells. In conclusion, this study has demonstrated that HIV-1 infects and replicates in oral mucosa epithelial cells in vivo and that these cells could represent a reservoir of the virus that may escape to the currently used antiretroviral therapy.

Topographic and quantitative display of integrated human immunodeficiency virus-1 provirus DNA in human lymph nodes by real-time polymerase chain reaction

In situ polymerase chain reaction (isPCR) has been applied in many fields that require detection of a genomic marker in combination with its topographic localization in tissue. We describe here a novel approach that circumvents the major drawbacks of in situ PCR, ie, low sensitivity, leakage of DNA from cells, and inability to quantify the DNA input. Frozen sections of a lymph node from a human immunodeficiency virus (HIV)-1-infected patient were fixed on glass microscope slides, and the glass was scored into square fragments of 0.5-mm edge length using a diamond cutting device. Slides were then attached to adhesive, elastic plastic foil and finally broken, and the foil was extended to allow sorting of fragments into PCR microtiter plates. The material was tested for HIV-1 proviral DNA by a sensitive real-time PCR protocol. Subjacent sections were stained for follicular dendritic cells to identify follicles. The fragmentation process prevented leakage of amplified DNA to neighboring areas as often experienced with in situ PCR. Provirus was clearly associated with follicular areas, in which provirus-carrying cells represented an average of 0.8% of the total cell population (peak density, 3.1% of all follicular cells). The results of this method suggest that the high density of provirus-containing cells in follicles may be important for the persistence of proviral DNA in infected persons.

Molecular biology of prostate cancer

Development of any cancer reflects a progressive accumulation of alterations in various genes. Oncogenes, tumour suppressor genes, DNA repair genes and metastasis suppressor genes have been investigated in prostate cancer. Here, we review current understanding of the molecular biology of prostate cancer. Detailed understanding of the molecular basis of prostate cancer will provide insights into the aetiology and prognosis of the disease, and suggest avenues for therapeutic intervention in the future.

Cell specific expression of CD10/neutral endopeptidase 24.11 gene in human prostatic tissue and cells

BACKGROUND

Neutral endopeptidase (NEP/CD10) is a cell surface zinc metalloproteinase that functions as part of a regulatory loop controlling local concentrations of peptide substrates and associated peptide-mediated signal transduction processes. In contrast to the encouraging data dealing with NEP activity and regulation in prostate epithelial cells, only a few studies are available on the cellular expression and localization of neutral endopeptidase in the prostatic stromal and cancer cells. Here, we describe the cellular localization of NEP in human prostatic tissue and cells using in situ RT-PCR as a novel molecular biological approach.

METHODS

Immunofluorescence and Western blot experiments were performed to control the expression and distribution of the NEP in normal and malignant human prostatic tissues and cell lines. NEP gene expression was monitored by RT-PCR, NEP mRNA was detected in paraffin tissue sections and cultured cells of human prostate by the highly sensitive method of one step-in situ reverse transcriptase-polymerase chain reaction (RT-PCR).

RESULTS

NEP mRNA was detected in human prostatic tissue and in cultured cells by means of in situ RT-PCR. Prostatic tissue showed strong signals in the glandular epithelium and weak signals in the stroma, cultured cells displayed strong signals in prostate cancer cells (LNCaP) and weak signals in stromal cells (hPCPs). Western blot experiments were performed using whole cell extracts to proof the presence of NEP protein in LNCaP and hPCPs. The experiments confirm the expression of NEP by both cell types, however, the experiment with hPCPs cells showed two bands. NEP-immunofluorescence was strong in normal prostatic epithelium and confined to the apical plasma membrane. In dedifferentiated prostate cancer specimens, immunofluorescence of apical plasma membranes was lost, and both the cytoplasm and portions of the plasma membrane were immunoreactive for NEP. Prostate cancer cells (LNCaP) showed a strong immunoreaction of the plasma membrane and the cytoplasm. In comparison with LNCaP cells, only a weak cytoplasmic immunofluorescence was found in some stromal cells (hPCPs).

CONCLUSIONS

In normal prostatic tissue and specimens derived from human prostate cancer, NEP mRNA and protein are expressed mainly by the epithelial cells and to a minor extent by the stromal cells of human prostate glands. In situ RT-PCR is a powerful and straightforward approach for the routine and rapid detection of cellular specific expression of low copy genes.

Detection of Trypanosoma cruzi DNA within murine cardiac tissue sections by in situ polymerase chain reaction

The use of in situ techniques to detect DNA and RNA sequences has proven to be an invaluable technique with paraffin-embedded tissue. Advances in non-radioactive detection systems have further made these procedures shorter and safer. We report the detection of Trypanosoma cruzi, the causative agent of Chagas disease, via indirect and direct in situ polymerace chain reaction within paraffin-embedded murine cardiac tissue sections. The presence of three T. cruzi specific DNA sequences were evaluated: a 122 base pair (bp) sequence localized within the minicircle network, a 188 bp satellite nuclear repetitive sequence and a 177 bp sequence that codes for a flagellar protein. In situ hybridization alone was sensitive enough to detect all three T. cruzi specific DNA sequences.

In-Cell PCR Method for Specific Genotyping of Genomic DNA from One Individual in a Mixture of Cells from Two Individuals: A Model Study with Specific Relevance to Prenatal Diagnosis Based on Fetal Cells in Maternal Blood

Background: During recent years, much attention has been paid to the possibility of using fetal cells circulating in the pregnant woman’s blood for prenatal diagnosis of genetic or chromosomal abnormalities. Although successes have been achieved in enrichment procedures for fetal cells from maternal blood samples, the use of such an approach for genotyping by molecular biology techniques in a more routine setting has been hampered by the large contamination of maternal nucleated blood cells in the cell isolates. Therefore, a new method based on in-cell PCR is described, which may overcome this problem.

Methods and Results: Mixtures of cells from two different individuals were fixed and permeabilized in suspension. After coamplification of a DNA sequence specific for one of the individuals and the DNA sequence to be genotyped, the two PCR products were linked together in the fixed cells positive for both DNA sequences by complementary primer tails and further amplification steps. In a model system of mixtures of male and female CD71-positive cells from umbilical cord blood attached to immunomagnetic particles, a Y-chromosome-specific sequence (TSPY) was linked to a polymorphic HLA-DPB1 sequence only in the male cells, leading to the correct HLA-DPB1 genotyping of the male by DNA sequencing of a nested, linked TSPY-HLA-DPB1 PCR product.

Conclusion: This approach might be usable on mixed cell populations of fetal and maternal cells obtained after conventional cell-sorting techniques on maternal peripheral vein blood.

A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea

Methanogens belong to the kingdom of Euryarchaeota in the domain of Archaea. The Archaea differ from Bacteria in many aspects important to molecular work. Among these are cell wall composition, their sensitivity to antibiotics, their translation and transcription machinery, and their very strict demands to anaerobic culture conditions. These differences may, at least partly, be responsible for the delay in availability of genetic research tools for methanogens. At present, however, the research within genetics of methanogens and their gene regulation and expression is in rapid progress. Two complete methanogenic genomes have been sequenced and published and more are underway. Besides, sequences are known from a multitude of individual genes from methanogens. Standard methods for simple DNA and RNA work can normally be employed, but permeabilization of the cell wall may demand special procedures. Efficient genetic manipulation systems, including shuttle and integration vector systems, have appeared for mesophilic, but not for thermophilic species within the last few years and will have a major impact on future investigations of methanogenic molecular biology.

Localization of transcripts corresponding to the major allergen from olive pollen (Ole e I) by electron microscopic non-radioactive in situ RT-PCR

In situ reverse transcription-PCR of mRNAs corresponding to the olive major allergen (Ole e I) has been tested at the ultrastructural level in mature olive pollen. The transcripts were present in the cytoplasm of both the vegetative and the generative cells, frequently associated to ribosomes in the endoplasmic reticulum. No labeling was detected in the pollen wall, nor in vacuoles, lipid bodies, plastids or mitochondria. Localization of the major olive allergen at ultrastructural level showed the protein present mainly in the lumen of the endoplasmic reticulum vesicles or pockets scattered in the cytoplasm, and in the outer region of the pollen exine. The results confirm the rough endoplasmic reticulum as the cell system involved in both the synthesis and storage of this protein. This is the first report of in situ RT-PCR on plant material at the ultrastructural level. The method described for mRNA amplification and detection is confirmed as a valuable tool for studying gene expression in plant material.

Application of in situ PCR to diagnose pneumonia in medico-legal autopsy cases

In situ polymerase chain reaction (in situ PCR) can detect specific sequences of DNA, such as those of micro-organisms in human tissue samples. In forensic medicine, there are many cases implicated with infection, and pneumonia is an especially common finding in autopsy cases. In the present study, we tried to detect the presence of bacterial infections in lung tissue samples. The experiment was performed with ten paraffin-embedded lung tissue samples, including three non-pneumonia cases using specific primers for Streptococcus pneumoniae, Staphylococcus aureus, Streptococcus equisimilis, and a DIG Oligonucleotide 3'-End Labeling Kit (Boehringer Mannheim). The findings showed that at least one or all three species of bacterial flora in the alveoli could be detected in all seven pneumonia cases, and that some leukocyte cytoplasms, after antigen-antibody and color emission chemical reactions, were also observed to have changed color due to phagocytosis. Detection of bacterial DNA in the leukocyte cytoplasm is a sign of vital reaction and differentiates between antemortem and postmortem infection. The present findings revealed that in situ PCR had the advantage that it helped identifying specific bacteria in the lung tissues with pneumonia.

Indirect RT-PCR in-situ hybridization: a novel non-radioactive method for detecting glucose-dependent insulinotropic peptide

To establish indirect in-situ PCR for the detection of intestinal peptide hormones, rat intestine and a murine intestinal tumor cell line, STC 1, were used. The results exhibited intensive staining of GIP-producing K-cells. Paraformaldehyde-fixed cryostat sections yielded the best results in signal to background ratio with RT-PCR in-situ hybridization. Moreover, it was possible to elevate the positive staining signal and to reduce background staining. Digoxigenin-labeled in-situ hybridization served as a control for specificity and sensitivity of GIP (glucose-dependent insulinotropic peptide) mRNA expression on cryostat as well as paraffin sections. In conclusion, this RT-PCR in-situ hybridization protocol proves to be a specific, sensitive and reliable non-radioactive technique for the detection of intestinal peptide hormone mRNA, especially in tissues or tumor cells where the application of ISH is limited.

Detection of human papillomavirus on Papanicolaou-stained cervical smears using indirect in situ polymerase chain reaction hybridization

OBJECTIVE

Polymerase chain reaction (PCR) and indirect in situ hybridization were combined to detect human papillomavirus (HPV) DNA on Papanicolaou (PAP)-stained cervical smears. To our knowledge, this is the first report of an experiment using indirect in situ PCR (IS-PCR) on PAP-stained cervical smears.

DESIGN

We collected native cell specimens from cervicovaginal lavage of 162 patients with squamous intraepithelial lesions. Solution-phase PCR (SP-PCR) was performed as the reference method in the detection of HPV DNA. Indirect IS-PCR was carried out for the same patients to detect the HPV DNA types 6/11 and 16/18 after the PAP-stained smears had been decolorized. Low-risk and high-risk HPV DNA types were also detected by both SP-PCR and indirect IS-PCR.

RESULTS

In the evaluation by indirect IS-PCR, 48 of 81 PAP-stained cell smears of low-grade squamous intraepithelial lesions were positive for HPV DNA, as compared to 40 positive cell smears determined by indirect SP-PCR (sensitivity of indirect IS-PCR compared to SP-PCR, 98.1%). Forty-two of 42 high-grade squamous intraepithelial lesion samples were positive for HPV DNA, as determined by both methods (sensitivity of IS-PCR, 100%). Cell lines investigated in this study as positive or negative controls for HPV DNA were confirmed by indirect IS-PCR and SP-PCR.

CONCLUSIONS

Our data show that in comparison to SP-PCR, indirect IS-PCR is a highly sensitive method to detect HPV DNA in cell smears from the uterine cervix. The advantages of indirect IS-PCR are (a) low numbers of cells needed, (b) the possibility of using PAP-stained specimens, and (c) cytologic details of smears can be preserved.

Analysis of gastrin receptor gene expression in proliferating cells in the neck zone of gastric fundic glands using laser capture microdissection

Gastrin stimulates proliferation of progenitor cells in the neck zone of gastric fundic mucosa. However, whether it directly enhances this proliferation through its receptors remains unclear. We investigated the expression of gastrin receptors in neck zone proliferating cells in rat gastric fundic glands using a reverse transcription polymerase chain reaction (RT-PCR) coupled with laser capture microdissection and in situ RT-PCR. Gastrin receptor expression was identified in c-fos-expressing cells located in the neck zone, and results of the RT-PCR analysis argued against contamination by other cells, such as enterochromaffin-like, parietal or D cells. Supporting this finding, gastrin receptor gene expression was identified in the neck zone as well as base glands by in situ RT-PCR. Therefore, it is suggested that proliferating cells in the neck zone are stimulated directly by gastrin via their gastrin receptors.

In situ reverse transcription-PCR for monitoring gene expression in individual Methanosarcina mazei S-6 cells

An in situ reverse transcription-PCR protocol for detecting specific mRNA in Methanosarcina mazei S-6 is described. This method allowed us to detect heat shock-induced increases in the intracellular levels of the transcript of the universal stress gene dnaK. The cell walls of paraformaldehyde-fixed cells were permeabilized by a thermal cycling procedure or by lysozyme treatment, and the cellular DNA was removed with DNase. The cells were subjected to a seminested reverse transcription-PCR protocol in which a digoxigenin-labeled primer was used. Detection of the reporter molecule was based on the 2-hydroxy-3-naphtoic acid-2'-phenylanilide phosphate-Fast Red detection system and binding of anti-digoxigenin-alkaline phosphatase conjugate. Fluorescence in permeabilized cells increased after a heat shock compared to fluorescence in non-heat-shocked cells, and the increase corresponded to an increase in the level of the dnaK transcript.

Light microscopic detection of BCR-ABL transcripts after in-cell RT-PCR: fusion gene expression might correlate with clinical evolution of chronic myeloid leukemia

A procedure for in-cell amplification of the hybrid BCR-ABL mRNA by reverse transcription and polymerase chain reaction (RT-PCR) without extraction of the nucleic acids was performed directly in fixed and permeabilized cells of leukemia patients (22 patients with Ph'-positive chronic myeloid leukaemia-CML and 1 with Ph'-positive acute leukaemia-AL, as well as 7 Ph'-negative cases) and Ph'-positive human leukaemia cell lines (K562, LAMA-84, BV173). The labelling of the amplified sequences was done employing biotinylated primers and a second PCR in a semi-nested fashion with a low number of cycles. An enzymatic system based on biotin-streptavidin-chromogen reaction was used for the detection of labeled PCR product, thus producing a coloured product, visible to the eye under a standard light microscope. All samples from patients with cytogenetic and molecular evidence of BCR-ABL rearrangement showed specific cytoplasmic staining at the site of the amplified hybrid transcripts. It allowed definite distinction between positive and negative cells. K562, LAMA-84, BV173 cells were characterized with strong diffuse staining while an interesting finding of the present study was the presence of variable quantities of colour product in patients' samples which might be due to different mRNA expression. Early and intermediate stages of myeloid maturation showed more intense reactivity. Cases with an aggressive course of accelerated or blast phase CML and AL were found to have a considerable subset of cells with strongly expressed signal while cases in chronic phase were characterised with uniform weak to moderate reaction. Our observations support the hypothesis that the amount of BCR-ABL transcript expression within neoplastic cells may play a role in dictating the eventual behaviour of the leukaemic clone. Future studies at a single cell level of larger series of consecutive cases with a follow up might be able to identify those patients who are prone to transformation and provide certain indications for further therapeutic decisions.

Development of a direct in situ RT-PCR method using labeled primers to detect cytokine mRNA inside cells

We have developed an original protocol of direct in situ RT-PCR with biotinylated labeled primers to detect cytokine mRNA inside cells. This label improved the specificity of the technique compared with the use of digoxigenin or fluorescein-labeled primers. We found a reliable correlation between the known expression of cytokine mRNA in a given cell and a positive signal with in situ RT-PCR. Nuclear counterstaining demonstrated that the positive signal obtained was distributed in the cytoplasm in accordance with mRNA localization. In addition, direct demonstration of the presence of the expected PCR product in cell extracts without non-specific parasitic DNA amplification provided strong support for the specificity of the method. Designing the primers in order to prevent DNA amplification, the use of recombinant Thermus thermophilus (rTth) DNA polymerase and a decreased duration of each cycle of PCR by combining the annealing and hybridization steps improved the reproducibility and reliability of the technique and morphological preservation of the cells. Experiments in which different proportions of cytokine mRNA positive and negative cells were mixed argue against significant diffusion of PCR product into initially cytokine mRNA negative cells, thereby leading to false-positive results. In comparison with the direct incorporation of labeled dNTP during amplification, our procedure appears to ensure greater specificity and does not need DNAse treatment which is often difficult to standardize. Detection of IL-2 and IFNgamma mRNA induction after T cell activation using this direct in situ RT-PCR method showed that the technique may be helpful for monitoring cytokine gene expression at a single cell level.

Intragenic recombinants of Plasmodium falciparum identified by in situ polymerase chain reaction

We report an in situ PCR technique for visualising amplified DNA of blood forms of Plasmodium falciparum on microscope slides by fluorescence microscopy. The method is used to assess the changes in frequency of different alleles of the MSP1 gene in cultures of the progeny of a cross. We show that parasites with a recombinant form of this protein possess an initial growth advantage before declining in numbers over the long-term.

Amplification methods to increase the sensitivity of in situ hybridization: play card(s)

In situ hybridization (ISH) has proved to be an invaluable molecular tool in research and diagnosis to visualize nucleic acids in their cellular environment. However, its applicability can be limited by its restricted detection sensitivity. During the past 10 years, several strategies have been developed to improve the threshold levels of nucleic acid detection in situ by amplification of either target nucleic acid sequences before ISH (e.g., in situ PCR) or the detection signals after the hybridization procedures. Here we outline the principles of tyramide signal amplification using the catalyzed reporter deposition (CARD) technique, present practical suggestions to efficiently enhance the sensitivity of ISH with CARD, and discuss some applications and possible future directions of in situ nucleic acid detection using such an amplification strategy.

CARD In Situ Hybridization: Sights and Signals

During the last decade, several strategies have been developed to improve the detection sensitivity of in situ hybridization (ISV) by amplification of either target nucleic acid sequences prior to ISH (e.g., in situ PCRX or the detection signals after the hybridization procedures (signal amplification). Here we outline the principles of tyramide signal amplification using the catalyzed reporter deposition (CARD) technique, summarize applications as well as possible limitations of CARD 15K, and discuss some future directions of in situ nucleic acid detection using this amplification strategy.

Molecular pathology in the preclinical development of biopharmaceuticals

Advances in cell and molecular biology have engendered a wide range of techniques that can be used to study the molecular events that underlie the cause of disease, thus producing a new field of study called "molecular pathology." These techniques can be either slide-based or non-slide-based (solution-based). The slide-based techniques include immunohistochemistry, in situ hybridization, and in situ polymerase chain reaction; pathologists play a unique role in the administration of these techniques because of their ability to interpret the end product (i.e., the slide). In this manuscript, we briefly discussed the use and impact of these slide-based techniques within all phases of drug development in the pharmaceutical industry.

Microscopic evidence against HIV-1 infection of germ cells or attachment to sperm

For a number of years we have intensively investigated the localization of HIV-1 in male genital tract tissues and secretions using a variety of microscopy techniques including immunocytochemistry, in situ hybridization, in situ PCR and electron microscopy. Our studies have failed to demonstrate an association between HIV-1 and either testicular germ cells or spermatozoa. In this article we present our results in the context of other related studies, and discuss the strengths and weaknesses of the techniques that have been used to address this important research question.

The in situ polymerase chain reaction for detection of chlamydia trachomatis

The in situ polymerase chain reaction (PCR) is a technique that has important applications in the diagnosis of viral and bacterial diseases. This study investigated an in situ PCR assay established to detect the presence of Chlamydia trachomatis in endocervical swabs. In addition, histological sections of endocervical squamous cell carcinoma were analyzed because previous studies had revealed a significant association with C. trachomatis. A total of 20 cervical neoplasms (squamous cell carcinoma in situ; n = 10; invasive squamous cell carcinoma; n = 10) and endocervical smears taken from five patients with and without inflammatory changes were analyzed by conventional PCR. Chlamydial DNA was found in 10 histological samples (six carcinomas in situ, four invasive carcinomas) and in one endocervical swab from a patient with known C. trachomatis infection. Positive specimens were used for establishing an in situ PCR assay (IS-PCR). After IS-PCR, these samples showed dense cytoplasmic staining of endocervical cells (smears) and non-neoplastic epithelial cells (cervical neoplasms). The other tumor samples and smears did not demonstrate positive PCR reaction. The results indicate that in situ PCR is an effective technique for localizing C. trachomatis in target cells because IS-PCR detection of chlamydial DNA correlated with histological and cytological features.

Hybridization-AT-tailing (HybrAT) method for sensitive and strand-specific detection of DNA and RNA

delta Tth DNA polymerase catalyzed polymerization of dATP and dTTP into a high-molecular-weight d(A-T) copolymer using oligo-d(A-T) as the template/primer (Hanaki et al., Biochem. Biophys. Res. Commun. 244, 210-219). Taking advantage of this reaction, we developed a highly sensitive method for strand-specific detection of DNA or RNA. The probe consisted of a 40- to 50-base-long complementary sequence on the 5' side and 10 repeats of AT on the 3' side. After hybridization using the 5' side, the 3' side AT repeat region was elongated by delta Tth DNA polymerase in the presence of the dATP, dTTP, and digoxigenin (dig)-11-dUTP. The elongation condition was 52-62 degrees C for 3 h. The method named HybrAT (hybridization-AT-tailing) was at least 100-fold more sensitive than the conventional hybridization with 5' end dig-11-dUTP labeled probe.

Demonstration of persistent enterovirus in the pancreas of diabetic mice by in situ polymerase chain reaction

BACKGROUND

Although Enterovirus (EV) do not persist in the tissue, which is essential to maintain autoimmunity, they have been associated as the cause of chronic autoimmunity in some cases of insulin dependent diabetes mellitus (IDDM). Convincing reports, demonstrating persistent EV infections in the pancreases, are rare.

OBJECTIVES

To determine the role of EV in IDDM, a mouse model was tested and i situ polymerase chain reaction (ISPCR) developed. The major problem of ISPCR are the high amounts of non-specific staining. In the current study we developed an ISPCR protocol which minimised non-specific staining and allowed the accurate localisation of the viral RNA in the tissue.

STUDY DESIGN

Five mice were infected with coxsackievirus group B4, sacrificed 7 weeks later and the pancreases were harvested. The EV nucleic acid were localised and detected in the pancreases by ISPCR.

RESULTS

In the current study non-specific staining of ISPCR, due to DNA repair and diffuse artefacts, were minimised and the EV nucleic acids were localised in the beta cells of the endocrine pancreases in all five diabetogenic mice.

CONCLUSION

This study demonstrates an association of viral RNA with the development of diabetes in mice and the usefulness of ISPCR to determine the role of EV in IDDM.

In situ amplification of the Epstein-Barr virus genome in cell suspensions

Epstein-Barr virus (EBV) is distributed widely throughout the world. Apart from a association with two geographically-restricted malignancies (Burkitt's lymphoma and nasopharyngeal carcinoma), EBV is thought to be implicated in the etiology of B-cell lymphoma in immunocompromised individuals. In these patients, monitoring the viral load in serum can provide useful information on the timing of the instigation of antiviral therapy, i.e. as soon as a rise is detected. PCR technology, owing to its high sensitivity, is used frequently in such situations. In order to gain further insight into the nature of the peripheral blood cells carrying the viral genome on a cell-by-cell basis, an in situ amplification technique was developed as a model using two cell lines growing in suspension, with the aim of distinguishing between EBV-positive and EBV-negative cells. Preliminary experiments were undertaken subsequently on clinical samples from patients with infectious mononucleosis and patients with lymphoma indicating that this technique might be useful clinically.

In situ PCR for in vivo detection of foreign genes transferred into rat brain

Here we describe the use of in situ PCR to detect a viral transgene in rat brain. Previously, we have reported in vivo gene transfer by using a defective herpes simplex viral vector in mammalian brain (Kaplitt, M.G., Pfaus, J.G., Kleopoulos, S.P., Hanlon, B.A., Rabkin, S.D., Pfaff, D.W., Mol. Cell. Neurosci. 2 (1991) 320-330). For detection of the LacZ transgene, we have used histochemical staining for the protein product, beta-galactosidase, and in situ hybridization for its mRNA, but the DNA itself cannot be reliably detected with conventional methods. Therefore we have adapted the technique of in situ PCR, so that we may detect minute quantities of transgenic vector DNA following in vivo gene. The brain sections, prefixed, were treated with PBS-detergent before PCR amplification to increase permeability for peptides and oligonucleotides across cellular barriers in brain tissue. Pretreatment with detergent retained better brain morphology than the more widely used proteinase treatment. The PCR mixture containing dNTPs, primers, digoxigenin-dUTP (Dig-dUTP) and buffer was loaded onto each brain section. Slides containing brain sections were placed in an aluminum boat and then on the block of the thermal cycler. Temperature was brought to 82 degrees C before adding Taq polymerase ('hot start' method). Dig-labeled PCR amplified fragments were then detected by alkaline-phosphatase-linked anti-digoxigenin-antibody. Positive signals were seen within the nucleus of transduced neurons, indicating presence of viral DNA. Enhanced specificity was observed with the use of Dig-labeled primers which eliminates the possibility of non-specific viral DNA detection through primer-independent reactions. Overall, this technique can serve not only as an internal control for transgene presence during comparisons of experimental groups of animals, but may also have clinical applications including the detection of viral infection in human brain such as HIV in pathology specimens.

A novel grid polymerase chain reaction (G-PCR) approach at ultrastructural level to detect target DNA in cell cultures and tissues

A novel grid polymerase chain reaction (G-PCR) method has been developed to be used at the ultrastructural level and with a high degree of resolution. Samples applied to test the method were fresh cell lines (CaSki, SiHa) and HPV-16 DNA-containing tissues rescued from routine paraffin blocks. The specimens were embedded in Epon-Araldite and/or hydrophilic-resin LRWhite. Ultrathin sections mounted on grids were subjected to G-PCR using an HPV-16-specific primer set. The amplified products were identified by auro-immunohistochemical labelling of the biotinylated nucleotide. The results indicated successful amplification of target DNA in both cell and tissue samples, being confined to the intranuclear region. The negative controls [HeLa cells, isolated mammary carcinoma cell cultures (MCF 7, and T47-D) (ATCC) (U.S.A.), normal thyroid tissue and steroid-producing tumour tissue] failed to exhibit any amplification of the target DNA sequences. The sensitivity of the G-PCR system was evaluated by performing a parallel in situ hybridization (ISH) of serial sections. The signals obtained from G-PCR were more intense than those of ISH and more informative as to the precise subcellular localization of amplicons.

Expression of herpes simplex virus DNA fragments located in epidermal keratinocytes and germinative cells is associated with the development of erythema multiforme lesions

Skin from acute and healed herpes simplex virus or herpes simplex virus-associated erythema multiforme (HAEM) lesions was examined by polymerase chain reaction with primers for DNA polymerase, ICP8, thymidine kinase (5' end of herpes simplex virus genome), and ICP27 (3' end of herpes simplex virus genome). The primers were herpes simplex virus specific and equally sensitive. The four herpes simplex virus genes were seen in acute herpes simplex virus lesions, but except for one patient, only polymerase (or polymerase and ICP8) were seen in 7-d healed lesional skin. Herpes simplex virus DNA was not seen 1-1.5 mo after healing. HAEM skins from 18 of 24 patients (75%) were positive for polymerase DNA and four of 24 (17%) were also positive for ICP8 or thymidine kinase DNA. Only one tissue (4%) was positive for polymerase, ICP8, and ICP27 DNA. Skin from healed HAEM lesions was still polymerase DNA positive 1-3 mo after lesion resolution. The polymerase DNA signal was in the basal and spinous cell layers of the epidermis and in the outer root sheath of the hair follicle. Polymerase RNA was identified by reverse transcriptase polymerase chain reaction in skin from acute, but not healed polymerase DNA positive HAEM lesions, suggesting that polymerase expression is associated with HAEM lesion development.

Study of adenovirus-mediated dystrophin minigene transfer to skeletal muscle by combined microscopic display of adenoviral DNA and dystrophin

In situ DNA hybridization of an E4 adenoviral sequence amplified by in situ polymerase chain reaction (PCR) was used to mark adenovirus-containing myonuclei in muscles of immunocompetent and immunosuppressed mdx mice following intramuscular injection of adenoviral recombinants. The adenoviral recombinants contained a 6.3-kb dystrophin cDNA (minigene) driven by a cytomegalovirus (CMV) promoter/enhancer and thus, immunostaining for dystrophin of the same sections permitted correlation of adenoviral recombinant-containing myonuclei with dystrophin positivity of the same muscle fiber segments. As early as 2 hr post-injection of adenoviral recombinant, an appreciable number of adenoviral recombinant-positive (AVR+) myonuclei, and some partial dystrophin positive (pdys+) fibers were observed. Some fully dystrophin-positive (dys+) muscle fibers were present as early as 6 hr. The maximum number of fibers containing AVR+ myonuclei (observed by 72 hr) was maintained until 60 days in immunosuppressed, but not in immunocompetent, animals. In immunocompetent animals, the maximum number of dys+ fibers was observed at 10 days. The vast majority of these fibers contained AVR+ myonuclei; however, by 60 days, dys+ fibers disappeared with some AVR+ myonuclei persisting. Our studies suggest that widespread delayed inactivation of the dystrophin expression cassette is probably unlikely. Thus, optimization of immunosuppression could assure successful long-term dystrophin gene transfer for gene therapy.

Improved methods for in situ enzymatic amplification and detection of low copy number genes in bacteria

We present alternative and improved protocols for in situ analysis of single copy genes in prokaryotes. Primed in situ amplification (PRINS) and cycle PRINS were used to detect, via the incorporation of a fluorescein labelled nucleotide, the presence of specific genes carried on both high and low copy number plasmids in individual cells of Escherichia coli and a marine bacterium, SW5. The optimised protocols described enabled a significant reduction in non-specific signals whilst maintaining high fluorescent activity via labelled nucleotide incorporation. In addition, nucleic acids were amplified linearly and were retained within the permeabilised microbial cells. These methods provide considerable advances in sensitivity, specificity and reliability compared to current protocols for bacterial in situ nucleic acid amplification.

Quantification of vitamin D receptor mRNA in tissue sections demonstrates the relative limitations of in situ-reverse transcriptase-polymerase chain reaction

In situ-reverse transcriptase-polymerase chain reaction (IS-RT-PCR) is a recently described technique that is used to localize low levels of mRNA within cells and tissue sections. One of the major criticisms levelled at this technique is that positive results may be meaningless, as amplification is required to demonstrate the transcripts of interest. The use of IS-RT-PCR to demonstrate mRNA for receptors for 1,25-dihydroxyvitamin D3 (VDR) in sections of human kidney and bone has previously been described. To ascertain whether the levels of VDR mRNA detected following IS-RT-PCR were transcriptionally significant, computerized image analysis was used to determine the mean silver grain density in human kidney and bone cells following conventional in situ hybridization and after various cycles of IS-RT-PCR. Only a few cycles of PCR were needed to produce an optimum signal, but amplification of signal following IS-RT-PCR was found to be relatively inefficient. Following the optimum number of cycles of IS-RT-PCR in kidney sections, there was a less than four-fold increase in signal. Similarly, in bone, the optimum signal detected was only approximately five times greater than that found with conventional in situ hybridization. These results clearly demonstrate that the increase in signal following IS-RT-PCR follows a more linear pattern and is relatively inefficient, compared with the usual exponential increase with conventional solution phase RT-PCR.

Direct in situ transcriptase polymerase chain reaction for the detection of Enterovirus genome in liver tissues

Adolescent female mice were inoculated intraperitoneally with coxsackievirus B3 Nancy strain, sacrificed 3 and 5 days later and the livers harvested. A protocol for direct reverse transcriptase in situ PCR (RT-ISPCR) detection of enteroviral RNA in paraffin-embedded liver tissues was developed. The optimal conditions for the assay were determined. The best results were obtained when the tissue was fixed in formalin, prior to being embedded in paraffin, then cut in 5 micron thick sections, and mounted onto silanized slides. After deparaffination the slides were incubated in 1 microgram/m1 Proteinase K for 10 min and cDNA synthesis was carried out. For successful RT-ISPCR 40-50 cycles of amplification were necessary. The optimal concentrations of dNTP, primers and Taq Polymerase for RT-ISPCR were determined by serial dilution assays. Primers were selected from highly conserved sequences in the 5' non-coding region (5'NTR). To detect the viral RNA in the liver, digoxigenin-dUTP was incorporated during amplification, subsequently bound with an antidigoxigenin antibody conjugated to alkaline phosphatase (AP), followed by colorimetric detection with nitroblue tetrazolium salt (NBT) and 5-brom-4chloro-3indolyl-phosphate (BCIP). The result was a blue precipitate in the cytoplasm of hepatocytes from infected mice. Fibroblasts, endothelial cells, lymphocytes and the nuclei of hepatocytes were negative. Thus, RT-ISPCR is a specific method for the detection of enterovirus RNA in the hepatocytes of infected mice, and can be of use for the determination of EV liver disease in man.

Demonstration of cytoplasmic tyrosinase mRNA in tissue-cultured cells by reverse transcription (RT) in situ polymerase chain reaction (PCR) and RT PCR in situ hybridization

To evaluate the specificity and applicability to the study of human tumor cells of the reverse transcription (RT) in situ PCR and RT polymerase chain reaction (PCR) in situ hybridization techniques, we examined five melanoma cell lines and five nonmelanoma lines for tyrosinase mRNA using primers specific for tyrosinase. Each procedural step was optimized and minutely controlled, and results from the in situ techniques and solution-phase RT-PCR were compared. All melanoma lines showed a specific pattern of perinuclear cytoplasmic reaction not seen in nonmelanoma lines. There was exact agreement between the results from the RT in situ PCR and RT-PCR in situ hybridization techniques and those from solution-phase RT-PCR. Ribonuclease digestion abolished cytoplasmic staining, as did omission of the reverse transcriptase step. Nuclear staining was seen in melanoma and nonmelanoma lines, apparently as a result of DNA synthesis from repair-replication and mispriming or nonspecific amplification. Neither high concentrations of deoxyribonuclease nor long incubation periods abolished this effect completely. Demonstration of cytoplasmic mRNA by RT in situ PCR and RT-PCR in situ hybridization specifically identifies cells of melanocytic lineage.

Demonstration of estrogen receptor mRNA in bone using in situ reverse-transcriptase polymerase chain reaction

Falling estrogen levels affect the female skeleton profoundly. Following menopause, estrogen lack is a major cause of osteoporosis. The site of estrogen action in human bone, however, is unclear, but responsive cells must express the estrogen receptor (ER). One obstacle to localizing these cells is that mRNA for ER is expressed in low copy number. Hence, conventional molecular techniques are either too insensitive to detect receptor transcripts (in situ hybridization) or necessitate amplification of RNA extracted from tissue [Northern analysis and polymerase chain reaction (PCR)], thus failing to identify the specific target cells within the mixed-cell population of bone. In situ PCR (IS-PCR) is a technique that combines the sensitivity of PCR with the localization of conventional in situ hybridization. The technique has previously been used primarily to detect single-copy genes and viral DNA within cells. More recently, incorporation of a reverse-transcriptase reaction (IS-RT-PCR) has allowed the technique to be used to identify rare mRNAs within tissues. We have therefore applied the technique of IS-RT-PCR to localize ER mRNA first in human breast tumors, a known positive tissue, and then in bone. Using conventional riboprobe in situ hybridization, ER transcripts were not detectable in any bone cells within sections taken from normal bone and several actively remodeling bone tissues, namely, Paget's disease, renal hyperparathyroidism, and healing fracture callus. The technique of IS-RT-PCR, however, allowed amplification of transcripts to a detectable level. Following two cycles of amplification, hybridization signal was observed in osteoblasts and to a lower level in osteoclasts and occasional osteocytes. This positive signal was more obvious after five cycles, particularly in osteoclasts and osteocytes. After ten cycles, although signal was increased in osteoclasts and osteocytes, it appeared to be decreased in osteoblasts, suggesting that overamplification leads to loss of target complex from these cells. We conclude that several cell types in human bone express ER mRNA in vivo.

Detection of proviral DNA of bovine leukaemia virus in cattle by a combination of in-situ hybridization and the polymerase chain reaction

Bovine leukaemia virus (BLV) proviral DNA was detected in lymphocytes isolated from cattle with persistent lymphocytosis (PL) by the polymerase chain reaction (PCR) and in-situ hybridization (ISH) with a biotinylated pX DNA probe. Many positive cells were observed when short-term culture and a combination of ISH with PCR were used. Immunohistochemical examination of lymphocytes isolated from the lymph node showed that BLV attached mainly to surface immunoglobulins (SIg) of positive B lymphocytes, and to a few tumour-associated antigen (TAA)-, PanT-, and CD8-positive cells and non-CD4 positive cells. Electron microscopical examination revealed colloidal gold particles within the nuclei and cytoplasm of lymphocytes. Lymphoid cells from neoplastic lymph node of enzootic bovine leukosis (EBL) cases gave particularly strong positive signals with the ISH-PCR method. The technique of combined ISH and PCR with a biotinylated pX probe may prove useful in future studies of EBL.

Direct in situ nucleic acid amplification: control of artefact and use of labelled primers

Aims-To evaluate factors which ameliorate false positive artefacts with direct in situ PCR using labelled dNTPs; to investigate the use of labelled primers to overcome this artefact whilst maintaining sensitivity.Methods-Sections of measles (RNA virus) infected Vero cells with cytoplasmic signal or cytomegalovirus (DNA virus) infected fibroblasts with nuclear signal were collected. In situ PCR (or in situ RT-PCR) was carried out by methods permitting evaporation. Reagents or conditions which may control false positive artefacts using labelled dNTPs were investigated systematically. Labelled primers were tested to overcome artefacts, with adjuncts which improve sensitivity.Results-No reagent nor condition investigated was able to control the artefact with labelled dNTPs. Excessive digestion and incomplete DNAse treatments exacerbated the artefact, whereas novobiocin decreased both specific signal and artefact. However, the artefact was controlled by labelled primers, albeit with relatively low sensitivity. Sensitivity using labelled primers could be increased using alcohol fixation, albumin or Perfectmatch.Conclusions-A repair process is implicated for the artefact using labelled dNTPs. Excessive digestion or DNAse treatment may exacerbate DNA damage by disrupting histones or the DNA, respectively. Labelled primers control this artefact, albeit with reduced sensitivity, which may be improved by precipitation fixatives (alcohol) and reagents which enhance specific reaction.