Human and viral gene detection in routine paraffin embedded tissue by in situ hybridisation with biotinylated probes: viral localisation in herpes encephalitis

Testing for HER2 in breast cancer

HER2 is a paradigm of a molecular target whose appropriate assessment is pivotal in the targeting of novel therapies for breast cancer, notably including Herceptin/Trastuzumab. Determining the correct levels requires immunohistochemical and molecular biological skills that are reproducible and measurable, coupled with a knowledge of the appropriate morphological and pathobiological context. Attaining these goals is not easy and laboratories testing for HER2 should maintain a high level of throughput of tests and engage in a recognized external quality assurance scheme. Fluorescence in-situ hybridization testing remains a particular challenge and there is a range of testing strategies. This testing forms the model for the identification of other novel molecular targets. In the future rapid throughput techniques such as real-time quantitative polymerase chain reaction (rqPCR), tissue microarrays or both should bring significant economies of cost and scale.

Just cool it! Cryoprotectant anti-freeze in immunocytochemistry and in situ hybridization

Immunohistochemical techniques offer specificity as well as flexibility for visualizing antigens. Their use with freely floating sections provides a high signal-to-noise ratio and has become a gold standard for brain and a number of other tissues. Yet this approach initially suffered from inability to keep the antigenicity in tissue sections and required immediate processing of all cut sections. Use of sucrose solutions enabled storage at refrigerator temperatures for a few days but longer-term storage was risky and either bacterial/fungal growth or evaporation of the storage solution compromised the integrity of the tissue. Our discovery 25 years ago that tissue sections can be stored for many years at -20 degrees C in an anti-freeze cryoprotectant solution with no loss of antigenicity solved this problem and has become widely used. More recently the utility of tissue stored for many years in anti-freeze cryoprotectant was pushed to new levels by testing new non-radioactive in situ hybridization (ISH) techniques that are based on modern immunocytochemistry. This review touches upon these advances in immunocytochemical technology using examples from neuroscience applications.

Confirmation of the copy number of chromosome 1 in interphase nuclei from paraffin sections of breast tumours by fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) was used to establish the copy number of chromosome 1 in a set of nine breast tumours in which the chromosome had previously been shown to have undergone a variety of rearrangements by loss of heterozygosity studies. In each case, FISH with satellite III DNA from chromosome 1q12 confirmed the results obtained by Southern hybridization. Importantly, in all five cases with rearrangements thought not to involve the centromeric region, FISH showed that the events had not disrupted the gross chromosome structure. This study highlights the potential of using the two techniques together to obtain a clearer picture of both large- and small-scale alterations to chromosomes in solid tumours.

Comparative analysis of human papillomavirus detection by PCR and non-isotopic in situ hybridisation

AIMS--To assess the relative diagnostic performance of the polymerase chain reaction (PCR) and non-isotopic in situ hybridisation (NISH) and to correlate these data with cytopathological assessment. METHODS--Paired analysis of human papillomavirus (HPV) detection was performed by PCR and NISH on exfoliated cervical cells from 122 women attending a routine gynaecological examination. PCR amplification followed by generic and HPV type specific hybridisation was compared with NISH on a parallel cervical smear. RESULTS--Overall, 32 cases were positive by NISH and 61 positive by PCR. Of the 105 cases in which both PCR and NISH were interpretable, 76 (26%) were normal smears, 20 of which were HPV positive by NISH and 37 (49%) by PCR. Of 17 borderline smears, two were NISH positive and 12 PCR positive. Eight of nine smears containing koilocytes were positive by NISH and seven by PCR. Of three dyskaryotic smears, none were NISH and two were PCR positive. The concordance of NISH and PCR in these samples was 57%. To assess sampling error, NISH and PCR were performed on an additional 50 cases using aliquots from the same sample. This increased the concordance between assays to 74%. Filter hybridisation of PCR products with the cocktail of probes used in NISH (under low and high stringency conditions) demonstrated that several cases of NISH positivity could be accounted for by cross-hybridisation to HPV types identified by PCR but not present in the NISH probe cocktail. CONCLUSIONS--Sampling error and potential cross-hybridisation of probe and target should be considered in interpretation of these techniques. PCR is more sensitive because it provides for the amplification of target DNA sequences. In addition, the PCR assay utilised in this study detects a wider range of HPV types than are contained in the cocktails used for NISH. However, PCR assays detect viral DNA present both within cells and in cervical fluid whereas NISH permits morphological localisation.

Criteria for consistent and high sensitivity of DNA in situ hybridization on paraffin sections: optimal proteolytic enzyme digestion

It is technically challenging for the detection of target DNA in low abundancy, such as viral DNA sequences in latently infected cells by nonisotopic in situ hybridization (ISH). Consistent result is even more difficult to achieve on routine paraffin sections. Proteolytic enzyme digestion is most critical for both consistency and sensitivity of the technique. We here have investigated the effect of enzyme digestion on cell morphology, protein and DNA reduction, and hybridization efficiency. The results demonstrated that enzyme digestion improves efficiency of ISH through a process involving partial DNA purification on sections. There is a clear relationship between proteolytic enzyme digestion, morphology changes, and hybridization efficiency. Although detection of DNA sequences in abundance can be achieved within a relatively wide range of digestion levels, maximum hybridization efficiency was always related to the cells, which showed morphology of nuclear swollen, weak homogeneous chromatin staining with hematoxylin and loss of visible nuclear membrane. Detection of viral DNA in low copy number critically depends on the creation of the morphologic changes by enzyme digestion. The morphological changes would therefore serve as important criteria for optimal digestion, result interpretation, and comparison.

Identification of aneuploid cells in cytological specimens by combined in situ hybridization and immunocytochemistry

The purpose of our study was the application of non-isotopic in situ hybridization with chromosome-specific repetitive DNA probes for the determination of cytogenetically aberrant cells in routine cytological materials, such as cervical smears and breast tumour aspirates. Hyperdiploid cells in fine needle aspirates (FNA) of breast tumours could be visualized by in situ hybridization with a chromosome 1-specific repetitive DNA probe. However, for the evaluation of a specific cell type in heterogeneous cell populations, i.e. cervical smears, a procedure combining immunocytochemistry and in situ hybridization can be required. Therefore, we developed a combination protocol using beta-galactosidase/ferri-ferrocyanide (blue-green) for immunocytochemistry and peroxidase/DAB (brown-black) for detection of the DNA probe. The described protocol enabled us to distinguish squamous epithelial cells within heterogeneous cell populations. By combining the chromosome 1 DNA probe with a specific cytokeratin marker it was possible to identify the chromosomal abnormal cells within cervical smears.

Mapping and chromosome analysis: the potential of fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) is a method widely used for the delineation of chromosomal DNA. FISH is applied in many areas of basic research as well as in clinical cytogenetics. In this review important technical improvements as well as the various applications of this method are summarized. In the first part different labeling and detection procedures are described and the potential of various kinds of probes are discussed. Recent developments in optical instrumentation and digital imaging procedures are outlined in the second part. The following important applications of FISH are discussed: (a) new strategies for high resolution mapping of DNA sequences; (b) detection of chromosomal aberrations in clinical material; (c) techniques allowing the simultaneous detection of numerous probes by multiple color FISH; and (d) the new approach of comparative genomic hybridization, allowing a rapid and comprehensive analysis of chromosomal imbalances in cell populations, which is particularly useful for the cytogenetic analysis of tumor samples.

Detection of genetic changes in Barrett's adenocarcinoma and Barrett's esophagus by DNA in situ hybridization and immunohistochemistry

We have investigated the occurrence of chromosomal DNA and cell cycle-related protein changes in Barrett's epithelium and adenocarcinoma. The presence of numerical chromosomal aberrations was studied by applying nonisotopic in situ hybridization (ISH) with (peri-)centromeric DNA probes, specific for chromosomes 7, 8, 17, and Y, to routinely processed tissue sections of five cases (4 male, 1 female) of Barrett's adenocarcinoma and adjacent Barrett's epithelium. Cell cycle-related protein expression was studied by immunohistochemistry (IHC) for p53 protein and the Ki-67 antigen (Mib-1) in subsequent sections. P53 protein overexpression was found in 3 of the 5 tumors. Overrepresentation of chromosome 8 and loss of chromosome 17 were found in 2 adenocarcinomas, both also negative for p53 protein overexpression. Y-loss, mostly clonal, was detected in 3 of the 4 male adenocarcinomas and 2 cases of adjacent Barrett's epithelium. One tumor had both areas of overrepresentation and loss of the Y chromosome. All Barrett's adenocarcinomas appeared to contain aneuploid cell populations. No relation was found between cell proliferation characteristics and chromosomal aberrations. We conclude that ISH with chromosome specific DNA probes can be applied for the assessment of potentially important numerical chromosome changes in Barrett's esophagus. Further, the combination of IHC and ISH is useful for evaluation of specific genetic events.

Identification of numerical chromosome aberrations in archival tumours by in situ hybridization to routine paraffin sections: evaluation of 23 phaeochromocytomas

We have applied non-isotopic in situ hybridization (ISH) to interphase cell nuclei of 23 phaeochromocytomas (18 primary and 5 metastatic tumours) within routine paraffin-embedded tissue sections. Each tumour was screened for numerical aberrations with a defined alphoid repetitive DNA probe set containing DNA probes specific for chromosomes 1, 7, 15, and Y. Normal adrenal medullas and other normal human cell types served as cytogenetic controls. Preservation of tissue morphology enabled targeted analysis of tumour cells. The presence of numerical chromosome changes in the tumour cells could easily be evaluated by comparing the ISH results of the DNA probes. Numerical abnormalities not previously reported in this neoplasm included overrepresentation of chromosomes 1 and 7, loss of chromosome 15, and both gain and loss of chromosome Y (P values < 0.01). The percentage of aneuploid cell nuclei in a tumour correlated well with the percentage of cells in the 4C peak of flow cytometric DNA histograms from these neoplasms. We conclude that interphase ISH can be used for the identification of new and reported cytogenetic changes in tumour cell nuclei within archival tissue sections. This novel procedure also allows for retrospective analysis of previously not karyotyped material.

Herpes simplex type 1 encephalitis in acquired immunodeficiency syndrome

A severe acute necrotizing herpes simplex virus type 1 encephalitis, apparently mediated by macrophages or cytokines or both, was seen in a patient with acquired immunodeficiency syndrome. The necrosis had a distribution similar to that seen in immunocompetent subjects. Viral inclusions were abundant and meningeal reaction was minimal, as previously described in one anergic patient.

Identification of hepatitis B virus-DNA in the liver by in situ hybridization using a biotinylated probe. Relation to HBcAg expression and histology

The cellular localisation of hepatitis B virus (HBV)-DNA in liver tissue was studied by in situ hybridisation using biotinylated and radiolabelled probes on samples from HBsAg carriers with a spectrum of disease and related to the presence of HBV-DNA in serum and intrahepatic HBcAg expression. Sixteen of the 31 patients studied were seropositive for HBV-DNA; nine had chronic active hepatitis and seven had chronic persistent hepatitis. HBV-DNA was detected in the liver tissue in seven of these patients. In each, HBV-DNA was detected in both cytoplasm and nuclei. All seven also had nuclear and/or cytoplasmic HBcAg which in six was associated with chronic active hepatitis. HBcAg (without tissue HBV-DNA) was detected in the remaining nine patients with an exclusively nuclear pattern in two. Fifteen patients were seronegative for HBV-DNA. HBV-DNA was not detected in the tissue of any of these. Three of these were HBcAg positive but in each this was confined to occasional nuclei and each had inactive disease. The close association between the presence of detectable HBV-DNA in tissue, cytoplasmic HBV-DNA expression and chronic active hepatitis in one group and a failure to detect HBV-DNA in those with nuclear HBcAg and benign disease suggests that there may be two distinct patterns of HBV replication in chronic HBV carriers which may influence the development of liver damage.

Spatial analysis of intranuclear human repetitive DNA regions by in situ hybridization and digital fluorescence microscopy

Non-isotopic (fluorescent) in situ hybridization has established itself as a useful technique for the localization of DNA sequences in both metaphase and interphase cells. The rapid development of digital fluorescence microscopy, especially confocal microscopy, has become a powerful aid for the evaluation of the hybridization results in cytogenetic and cell biological applications. In this review we will demonstrate the utility of these methodologies for the three-dimensional visualization and analysis of chromosome-specific (peri)centromeric repetitive DNA sequences within the intranuclear structure of human cells and cell lines.

Bcl-2 proto-oncogene expression in Epstein-Barr-virus-associated nasopharyngeal carcinoma

The bcl-2 proto-oncogene product inhibits apoptosis. Increased levels of bcl-2 protein are associated with prolonged B-cell survival and have been demonstrated in a high proportion of follicular B-cell lymphoma. Recent studies have shown that bcl-2 protein expression in B cells immortalized by Epstein-Barr virus (EBV) in vitro is up-regulated by the EBV-latency-associated antigen, latent membrane protein (LMP) 1. The epithelial malignancy, undifferentiated nasopharyngeal carcinoma (UNPC), has a well-established association with EBV and the tumour cells characteristically display a restricted latent viral phenotype including LMP 1. This study has investigated the relationship between the presence of EBV DNA, EBV phenotypic profiles and bcl-2 protein expression in conventionally processed and cryopreserved samples of NPC using in situ hybridization, immunocytochemical and immunoblotting techniques. bcl-2 was detected in most (80%) samples of UNPC as well as in 1/3 samples of keratinizing NPC and 2/2 samples of nasopharyngeal adenocarcinoma. However, no close correlation was found between the presence of EBV DNA, and profiles for LMP 1 and bcl-2 protein expression in 45 UNPC. In addition, bcl-2 protein was shown to be selectively expressed in the basal compartment of normal nasopharyngeal epithelia. bcl-2 protein expression has not been reported previously in malignant tumours of epithelial origin. The findings in this study implicate a role for bcl-2 both in normal keratinocyte differentiation and in the pathogenesis of epithelial malignancy.

Interphase cytogenetics in paraffin sections of lung tumors by non-isotopic in situ hybridization. Mapping genotype/phenotype heterogeneity

To better understand the relationship between specific chromosome changes found in human lung tumors and their phenotypic consequences at the tissue level, an in situ hybridization procedure was optimized for use on formalin-fixed paraffin-embedded tissue sections of human lung tumors. Pretreatment heating of sections, pepsin concentration, duration of pepsin treatment, hybridization conditions, and posthybridization washing conditions were varied to determine optimum conditions. The deparaffinized sections were stained with centromeric probes for chromosomes 7 and 17, and a chromosome index for each tumor was derived by dividing the mean number of chromosome signals found on the tumor cells by the mean number of chromosome signals on normal cells (lymphocytes and fibroblasts) in the same section. This chromosome index was then compared with the DNA index determined in an adjacent section by Feulgen staining followed by image analysis quantitation. The chromosome index correlated well with the DNA index, but in some cases, chromosome 7, or 17 in other cases, was either over- or under-represented compared with the corresponding DNA index. In addition, chromosome and DNA alterations were shown to be differentially expressed within the same tissue section, correlating with a change in tumor differentiation status. These results suggest that in situ hybridization will prove to be an important tool for determining the underlying genetic basis for tissue phenotype heterogeneity by allowing genetic determinations to be made on paraffin-embedded tissue sections where tumor histological architecture is preserved.

Histological preservation after in situ hybridization to archival solid tumour sections allows discrimination of cells bearing numerical chromosome changes

In this study, non-isotopic in situ hybridization (ISH) was used for the cytogenetic and histological examination of urological (prostatic adenocarcinoma) and endocrine (phaeochromocytoma) tumour cell nuclei in 4 microns paraffin-embedded tissue sections. In order to investigate preservation of tissue morphology, standard heat denaturation was compared with a mild enzymatic treatment for the production of single-stranded (ss)-DNA for ISH. Numerical analysis by ISH with chromosome-specific repetitive DNA probes for chromosomes 1, 7, and 11 revealed overrepresentation of chromosome 7 in the phaeochromocytoma (P < 0.01). The constitutional underrepresentation of the Y chromosome was easily detected in the prostate tumour (P << 0.01) when probed for chromosomes 7, 16, and Y. The enzymatic treatment appeared superior to heat denaturation with respect to tissue architecture in the phaeochromocytoma, while no clear difference was observed in the prostatic cancer. ISH probe patterns were similar for the two types of denaturation in both tumours (P > or = 0.20). We conclude that (1) ISH can be used for the identification of numerical cytogenetic changes in solid tumour cell nuclei within archival tissue sections; and (2) mild 'denaturation' protocols, replacing heat, are preference in retaining tissue architecture in fragile tumour specimens.

Comparative analysis of human papillomavirus detection by dot blot hybridisation and non-isotopic in situ hybridisation

AIMS

To determine the relative diagnostic performance of non-isotopic in situ hybridisation (NISH) and a dot-blot assay for detecting human papillomavirus (HPV) on exfoliated cervical cells; and to correlate the results with cytopathological assessment.

METHODS

Cervical smears and cytological samples were obtained from 122 patients during the same clinical examination and the presence of HPV sequences determined by NISH and dot-blot analysis, respectively.

RESULTS

Dot-blot analysis gave an autoradiographic signal in 15 of 121 (12.4%) cases, while NISH detected viral genomes in 38 of 114 (33.3%) cases. Even in the presence of koilocytosis, where vegetative replication of the virus occurs, NISH was positive in over twice as many cases as dot-blot analysis (NISH 90%, dot-blot 40%), while in smears within normal cytological limits, where the viral copy number is likely to be considerably lower, the differences were more striking (NISH 31%, dot-blot 5%).

CONCLUSIONS

These data show that NISH on cytological smears is more sensitive than a standardised dot-blot hybridisation assay for detecting HPV infection in cytological material and is therefore a more appropriate screening tool.

Detection of high risk human papillomavirus in routine cervical smears: strategy for screening

AIM

To develop a methodology for direct detection of high risk human papillomavirus (HPV) infection in routine cervical smears by non-isotopic in situ hybridisation (NISH) which can be compared with cytopathological assessment of the same cells.

METHODS

The methodology was established using cultured cells and routine cervical smears hybridised with digoxigenin labelled probes for HPV, 16, 18, 31, and 33. The technique was applied to the analysis of 53 patients from a sexually transmitted disease clinic.

RESULTS

The optimal sensitivity achieved for single HPV detection in cultured cells was 1-2 copies of HPV 16 per cell and that for detection of a cocktail of HPV types in routine cervical smears was 2.5-12 copies per cell. Of parallel smears taken from patients with a normal Papinacolau-stained smear 33.3% (24) contained a HPV 16, 18, 31, and 33 signal indicating an occult HPV infection. The prevalence of these HPV types was similar in women in whom a cytopathological diagnosis of wart virus infection was made (64.7%, 17) and in patients with mild dyskaryosis (75%, 12).

CONCLUSIONS

The methodology evolved localises HPV sequences directly to epithelial cell nuclei, which can be morphologically assessed by haematoxylin counterstaining. Sample contamination with exogenous viral sequences can be distinguished from true infection. In this study, a HPV signal was not found in morphologically normal epithelial cells. The methods described will permit the detection of HPV sequences in routinely collected cervical smears and the evaluation of the natural history and potential clinical relevance of HPV infection without changes in clinical practice.

Screening for high- and low-risk human papillomavirus types in single routine cervical smears by non-isotopic in situ hybridization

Routine cervical smears (n = 262) from a Sexually Transmitted Diseases clinic were screened by non-isotopic in situ hybridization (NISH) stratifying human papillomavirus (HPV) infections into HPV6/11 (low risk) and HPV16/18/33 (high risk) categories. Of 188 patients with cytologically normal smears, HPV sequences were demonstrated in 41%. Of the 128 cases analysed by dual NISH, 16% contained low risk, 20% high risk and 5% both groups. In patients with cytological evidence of wart virus infection (WVI) only, 54% (n = 50) contained high-risk and 22% low-risk HPV types. The comparable incidences in CIN1/2 plus WVI (n = 24) were not significantly different: 54% and 17%, respectively. Cytological criteria underestimate the prevalence of HPV infection in patients with cytologically normal smears. This represents either 'occult' or 'latent' infection. The identical prevalence of HPVB16/18/33 in WVI only, and CIN1/2 plus WVI, suggests that the cytopathic effect induced by these HPVs may represent one end of a spectrum of morphological change which progresses to cervical intraepithelial neoplasia (CIN).

Detection of human papillomavirus in matched cervical smears and biopsy specimens by non-isotopic in situ hybridisation

AIMS

To determine the relative diagnostic sensitivity of non-isotopic in situ hybridisation (NISH) for the diagnosis of human papillomavirus (HPV) on matched smears and biopsy specimens; to compare the NISH signal type in the two samples; and to correlate the NISH data with the morphological diagnosis.

METHODS

HPV samples were assayed individually by NISH with digoxigenin labelled probes (HPV6, 11, 16, 18, and 33) on routinely collected paraffin wax embedded cervical biopsy specimens and for high risk HPVs with a cocktail of similarly labelled probes (HPV16, 18, 33) on matched smears. These were taken at the same colposcopic examination from 32 patients investigated for an abnormal cervical Papanicolaou (PAP) stained smear.

RESULTS

An HPV signal was present in 18 (56%) biopsy specimens and in 14 (44%) smears. There was higher concordance of sets of data in the presence of cytopathic wart virus changes. The superiority of biopsy over smear in detecting HPV was mainly the result of examining the entire cervical biopsy specimen rather than cells scraped from the cervical surface. The NISH signal type in both biopsy specimen and smear was similar; it has been shown that NISH type 1 signal correlates with episomal viral replication and type 2 and 3 signals with viral integration.

CONCLUSIONS

These data show that NISH on cervical smears is a worthwhile primary screen for HPV infection. The NISH signal types in cervical smears are similar to those previously described in cervical biopsy specimens.

Detection of gastrin and its messenger RNA in Zollinger-Ellison tumors by non-radioactive in situ hybridization and immunocytochemistry

Gastrin immunocytochemistry and non-radioactive in situ hybridization, using biotinylated oligonucleotide probes, for gastrin mRNA have been used for studying a retrospective material of six gastrin-producing (Zollinger-Ellison) tumors. Hybridization results for gastrin mRNA were positive in all six, while gastrin immunoreactivity could be detected in five tumors. In one of the patients, different areas of the same tumor displayed differences in immunoreactivity to gastrin, but were uniformly hybridization positive. Weak hybridization signals were detected in liver metastases from a necropsy case, while the gastrin immunostaining was more pronounced. The results show that non-radioactive hybridization methods are applicable to routine clinical specimens stored for as long as 16 years and that in situ hybridization may be a useful complement to immunocytochemical diagnosis, particularly in cases where high synthesis and little storage of hormonal products occur.

Comparison of immunocytochemistry and in situ hybridization in the cytodiagnosis of genital herpetic infection

Over a 62-month period, 53 patients were found to have cervicovaginal smears that contained cells consistent with, or equivocal cells for, a herpes simplex virus (HSV) infection. The Papanicolaou-destained smears from these cases were restrained in situ hybridization (ISH) with a biotinylated cloned DNA probe and immunocytochemistry (ICC) assay and were compared for the detection of HSV in cervicovaginal smears by two methods. Cytological findings classified the 53 slides into two groups, i.e., cytologically herpes positive (33 patients) and equivocal cases (20 patients). Each group was subdivided into two groups: group A was confirmed by ICC, and group B was confirmed by ISH technique. Of the 33 cellular samples containing cells considered to be consistent with a herpes infection, 15 (88%) of 17 were positive by means of ICC technique (group A), 6 (43%) of 14 were positive by ISH technique (group B). Of the 20 smears showing equivocal cell changes thought unlikely to be caused by an HSV infection, 6 (60%) of 10 were positive by ICC (group A), 2 (29%) of 7 were positive by ISH (group B). With the ISH technique, five smears showed dislodged cells from glass slides due to enzyme treatment and denaturation. The results revealed that the ICC technique is a rapid and reliable procedure and thus recommended for routine diagnosis of HSV infection. Moreover, ICC is easier to perform and interpret and is less expensive than ISH. Therefore, the ICC may be preferable to ISH for detecting HSV in routine Papanicolaou diagnostic work.

Detection of mRNA encoding crustacean hyperglycemic hormone (CHH) in the eyestalk of the crayfish Orconectes limosus using non-radioactive in situ hybridization

A non-radioactive in situ hybridization procedure for the localization of the mRNA encoding the crustacean hyperglycemic hormone (CHH) in the eyestalk of the crayfish Orconectes limosus has been developed. Based on the partial amino acid sequence of CHH, polymerase chain reactions were performed to generate complementary DNA (cDNA) clones encoding CHH. Non-radioactively labelled probes derived from the cDNA sequence were used to establish suitable conditions in terms of tissue fixation and pretreatment for detection of the CHH-encoding mRNA in combination with an immunocytochemical staining using a polyclonal antibody for CHH. Localization of the mRNA in the CHH perikarya was obtained with a complementary RNA probe in combination with pepsin/HCl treated Bouin-fixed eyestalks. The immunocytochemical staining confirmed that this cRNA probe specifically hybridized with mRNA of cell somata belonging to the CHH-producing cell system in the eyestalk of Orconectes limosus.

In situ hybridisation in perspective

In the introduction to this review two questions were posed: is the technology associated with ISH ready for general use, and will the method become an important investigative tool? With the exception of the demonstration of some single and low copy sequences, non-radioactive ISH is now sufficiently developed and simplified to make it a routine technique. It is also clear that ISH will continue to have an important research role. In diagnostic pathology the technique is already providing valuable information and the present decade should see the development of many more diagnostic applications.

The use of molecular techniques in studying viral pathogenesis in the nervous system

Molecular biological techniques have been used extensively to gain insights into the pathogenesis of a variety of diseases caused by neurotropic viruses. Increasingly sensitive methods for detecting viral nucleic acids and proteins in pathological nervous tissues have clarified the viral aetiology of certain neurological disorders and are now being used to investigate possible viral involvement in others. In addition, a diverse range of molecular techniques has greatly enhanced our understanding of the molecular basis of viral neurotropism and neurovirulence in both humans and experimental animals. This article provides an overview of these various approaches with examples drawn from both clinical neurological disease and animal models.

Human papillomaviruses in anogenital warts in children: typing by in situ hybridisation

OBJECTIVE

To identify the types of human papillomaviruses found in anogenital warts in children and to relate these to clinical and social information.

DESIGN

In situ hybridisation using biotin labelled DNA probes to 11 types of human papillomavirus was performed on biopsy specimens from 17 children with anogenital warts.

SETTING

Nuffield department of pathology and the department of dermatology, Oxford.

PATIENTS

Children in one group were referred by general practitioners or paediatricians to the dermatology department, where biopsies were performed. The other children were seen in four different hospitals, and biopsy specimens were submitted to the laboratory at the physician's or pathologist's request.

RESULTS

Of the 17 biopsy specimens, 10 contained cells positive with a probe to a genital human papillomavirus type (types 6 or 11), while six were positive with a skin virus type (types 2 or 3). One was negative. The virus type present bore no relation to the site or appearance of the warts. The virus type did, however, appear to correlate with groups of children. Skin types were commoner in older children (over 4 years), in those with a relative who had skin warts, and in children with warts elsewhere; there was no relation with the child's sex and no suspicion of sexual abuse in these children. These circumstances suggested non-sexual transmission, such as autoinoculation. In contrast, genital types were commoner in girls, in children under 3 years, in children with relatives with genital warts, and in those with no warts elsewhere. Nevertheless, there was suspicion or evidence of sexual abuse in only half these children, suggesting that other routes of transmission--for example, perinatal--might have been implicated.

CONCLUSION

Anogenital warts in children may contain either skin or genital wart virus type. Although the type of human papillomavirus present may give some indication of the likely mode of transmission, this can be interpreted only in conjunction with all available clinical and social information. The type of virus does not provide proof of the presence or absence of sexual transmission.

In situ hybridisation in herpetic lesions using a biotinylated DNA probe

In situ hybridisation was performed with a biotinylated DNA probe for herpes simplex virus (HSV) using high temperature denaturation on formalin fixed, paraffin wax sections of lung, brain, ganglion and keratinising and non-keratinising squamous epithelia. Eosinophilic viral nuclear inclusions or characteristically moulded multiple nuclei with altered chromatin, which were present in two cases of HSV encephalitis and one case of viral pneumonitis, all showed complete hybridisation visualised by an alkaline phosphatase/nitroblue tetrazolium detector system. HSV encephalitis and trigeminal ganglionitis, which were confirmed serologically or clinicopathologically but lacked nuclear changes, also gave positive dense nuclear signal in neurons, glias and satellite cells. No staining was present in the ganglion cells in trigeminal zoster, the glia in progressive multifocal leucoencephalopathy, or in a variety of cells in a lung coinfected with cytomegalovirus. In 10 herpetic blisters of squamous epithelia, infected cells hybridised strongly, while morphologically similar herpes zoster lesions remained negative. In neural tissues non-hybridisation staining was most obtrusive in corpora amylacea and seemed to reflect nonspecific probe adherence. In squamous epithelium, major non-hybridisation staining was caused by probe and antibody possibly adhering to intracellular keratin. The HSV probe permits specific detection of virus in the absence of characteristic nuclear changes and allows varicella zoster virus to be differentiated from HSV, provided that the aforementioned problems with non-hybridisation staining are borne in mind.

Detection of cytomegalovirus-infected cells in autopsy material by in situ hybridization

A non-radioactive in situ hybridization (ISH) method was elaborated to detect cytomegalovirus (CMV)-infected cells in tissue specimens processed for diagnostic routine histopathology. A biotinylated CMV-DNA probe was hybridized following a) four different enzymatic predigestions, b) progressively increasing denaturation periods, and then detected by c) streptavidin-biotin, d) a monoclonal antibody against biotin using a three-stage alkaline phosphatase anti-alkaline phosphatase (APAAP)-technique, and e) combining c + d. Autopsy specimens obtained from an infant with acquired CMV-infection, six patients with AIDS, five patients clinically and serologically without CMV-infection, and preoperative needle core biopsies from six renal allografts served as material. ISH was specific and more sensitive when compared to immunohistochemical (IMH) detection of CMV-antigens by a monoclonal antibody. ISH was concluded to be a rapid, practical, and sensitive tool in daily diagnostic histopathology.

Use of immunocytochemistry and biotinylated in situ hybridisation for detecting measles virus in central nervous system tissue

Optimised immunocytochemical (ICC) and in situ hybridisation (ISH) protocols for long term, formalin fixed, central nervous system tissue infected with measles virus were developed. The effectiveness of 10 proteases for the enzymatic unmasking of formalin fixed antigen and nucleic acid was investigated. Protease VIII gave maximal signal generation with optimal tissue preservation and no background staining for both techniques. The use of a microwave oven as an additional pre-hybridisation step for RNA-RNA in situ hybridisation produced a significant increase in the number of cells labelled for genomic RNA. The ability to show the presence of antigen and nucleic acid in long term, formalin fixed tissue facilitates the use of stored necropsy material available in pathology departments for ICC and ISH investigations.

Comparison of in situ hybridization and immunohistochemistry for detection of cytomegalovirus and herpes simplex virus

In situ hybridization (ISH) and immunohistochemistry (IHC) were compared for detection of cytomegalovirus (CMV) and herpes simplex virus (HSV) in routinely processed tissue. Fifty-four formalin-fixed paraffin-embedded tissue samples infected with CMV (36 tissues) or HSV (18 tissues) from 30 autopsies were studied. All tissues had either positive viral cultures (38 of 54) or characteristic viral inclusions on hematoxylin and eosin examination (39 of 54). The tissues examined included lung (28), liver (nine), kidney (five), heart (three), adrenal (two), spleen (two), and thymus, pancreas, appendix, esophagus, and duodenum (one each). Studies by ISH were performed with two detection systems, using biotinylated probes to CMV and HSV (Enzo Biochem, New York, NY). Using ISH with an alkaline phosphatase detection system, infected cells were detected in 33 of 54 tissues (CMV: 23 of 36, HSV: 10 of 18). Using ISH with a peroxidase detection system, infected cells were identified in 30 of 54 tissues (CMV: 22 of 36, HSV: eight of 18). With IHC, antibodies to CMV and HSV stained the infected cells in 34 of 54 tissues (CMV: 24 of 36, HSV: 10 of 18). All infections detected with ISH were also detected with IHC. We conclude that these techniques for ISH and IHC are equally effective for detecting CMV and HSV in paraffin sections. The results of both techniques correlate better with viral inclusions than with culture results. The ISH stains are more difficult to prepare and in some cases are more difficult to interpret. Therefore, IHC may be preferable to ISH for detecting CMV and HSV in routine diagnostic work.

Optimization of non-radioactive in situ hybridization: image analysis of varying pretreatment, hybridization and probe labelling conditions

Using detection of proopiomelanocortin (POMC) mRNA in rat pituitary as a model, varying conditions of tissue pretreatment, hybridization and probe labelling have been tested. Results were evaluated both by visual assessment and by image analysis of coded specimens. Good correlations between visual gradation, optical densities and cell area percentages were obtained. However, determinations of optical densities (or pixel values) provided most detailed information. The data obtained emphasize the interdependence of fixation and permeabilization conditions and clearly show that the stronger the primary fixation, the more efficient the permeabilization by proteinase K must be. The hybridization temperature is also of importance and temperatures between 40-45 degrees C produced the best signal to noise ratio. The POMC-directed 24-mer probe had a theoretical melting point (Tm) of 49.4 degrees C (in the absence of formamide) and four individual experimental determinations of Tm produced a mean value of 48.9 degrees C. Detection of the biotinylated probe was best accomplished with monoclonal antibiotin antibodies and the alkaline phosphatase-anti-alkaline phosphatase (APAAP) system. Short washes at high-stringency (0.1 x SSC, 45 degrees C) produced an optimal signal to noise ratio. Inclusion of 50% formamide in the hybridization buffer produced an enhanced signal to noise ratio, in spite of a higher background staining. The probe employed for most studies was a synthetic 24-mer oligodeoxynucleotide, complementary to the MSH[4-11]-coding region of POMC mRNA. It was labelled with biotinylated dUTP and unlabelled dCTP using terminal transferase. Chromatographical analyses revealed the labelled probe to be heterogeneous in tail length.(ABSTRACT TRUNCATED AT 250 WORDS)

Anal cancer and human papillomaviruses

Epidemiologic and clinical evidence has suggested a possible association between anal cancer and human papillomavirus (HPV) types that are known to be associated with cervical and other genital cancers. Using Southern blot and dot blot analysis, the authors examined 45 primary anal malignancies for HPV DNA types 6, 11, 16, and 18. HVP 16, DNA was detected in 23 of 41 (56 percent) anal squamous-cell carcinomas (SCC) and in the lymph-node metastases of two of these tumors. In addition, HPV 18 DNA was detected in 2/41 (5 percent) anal SCCs. Anal SCC contained no detectable HPV 6 or 11 DNA. The remaining four primary anal malignancies were not squamous carcinomas and did not contain any detectable HPV DNA. Nonmalignant anal epithelium and malignant rectal mucosa obtained from surgical patients undergoing hemorrhoidectomy and abdominoperineal excision of the rectum did not contain any detectable HPV DNA. HPV 16 DNA in anal cancer was predominantly integrated into the host cell DNA. In situ hybridization was used to demonstrate that HPV 16 DNA in anal SCC tissues is confined to the nuclei of carcinoma cells. The results of this investigation closely parallel similar studies of cervical cancer and lend support to the concept of the involvement of HPV 16 and 18 in the development of anal and genital squamous-cell carcinoma.

Detection of numerical chromosome aberrations in bladder cancer by in situ hybridization

The nuclear DNA content of 53 transitional cell carcinomas (TCCs) of the urinary bladder, as determined by flow cytometry (FCM), was compared with chromosome ploidy as detected by nonradioactive in situ hybridization (ISH). For this purpose, probes for repetitive DNA targets in the (peri) centromeric region of chromosomes 1 and 18 were used. Hybridization results with both probes of 35 TCCs, which had a DNA index of approximately 1.0 as concluded from FCM, showed evident chromosome 1 aberrations in approximately 25% of the tumors, and in a few cases an aberration for chromosome 18 was detected. Comparison of the ISH spot numbers for both chromosomes showed in most cases a higher number for chromosome 1 than for chromosome 18. ISH on 18 cases of TCCs, which showed a single peak in FCM with a DNA-index of 1.2 to 3.2, exhibited a profound heterogeneity. In these TCCs the ratio between chromosomes 1 and 18 varied over a wide range, resulting in cases showing more hybridization signals for chromosome 1 than for chromosome 18 or the opposite. Furthermore, using ISH minor cell populations showing polyploidization and giant cells containing numerous ISH signals could occasionally be detected. Results showed that interphase cytogenetics by ISH enable a fast screening of numerical chromosome aberrations and detection of different cell populations within one tumor, which was apparently homogeneous according to FCM.

Detection of reactivating pseudorabies virus in tissue by immunoperoxidase technique

Reactivation of pseudorabies virus (PRV) was induced in pigs by prednisolone treatment. The virus was re-isolated from nasal secretions of four, brain cortex of two and mandibular lymph node of three out of 12 pigs, respectively. The characteristic lesion of recurrently infected pigs was focal necrosis in the brain cortex and mandibular lymph node, accompanied by reactivating virus particles in the degenerating cells. Coincident with the pathological lesions, PRV antigen was detected in two of the brain cortex and six of the mandibular lymph node specimens by immunoperoxidase staining. These results suggest that the immunoperoxidase technique was more sensitive than virus isolation for demonstrating the reactivity of PRV in recurrently infected pigs.

Detection of cytomegalovirus antigens and DNA in tissues fixed in formaldehyde

Immunohistochemical techniques with monoclonal antibodies against cytomegalovirus (CMV) immediate early (IEA) and early antigens (EA), and in situ hybridisation, were used to detect CMV infection in routinely obtained, formaldehyde fixed and paraffin wax embedded tissues taken from bone marrow transplant patients, who had died form interstitial pneumonia. To improve the rates of detection of CMV-IEA and EA the wax embedded material was pretreated with 0.4% pepsin/HCl at 37 degrees C for 30 minutes. This pretreatment was also advantageous for in situ hybridisation. In the patients with histological evidence of CMV infection or positive viral culture from the lung tissue, or both, viral proteins and nucleic acids were detected in lung, as well as in other organs. Immunohistochemical techniques proved superior in heavily infected but necrotic tissues. In control patients (patients who had died from interstitial pneumonia without any evidence of CMV, or with no interstitial pneumonia at all) in situ hybridisation showed no positive signal, while immunohistochemical techniques showed only a few positive cells in lung tissue of one of nine patients. In addition to CMV-DNA analysis, formaldehyde-fixed, paraffin wax embedded tissue is amenable to immunohistochemical analysis with CMV monoclonal antibodies.

In situ hybridization: an optimised detection protocol for a biotinylated DNA probe renders it more sensitive than a comparable 35S-labelled probe

The development of a highly sensitive biotinylated in situ hybridization protocol using egg drop syndrome virus infection of domestic fowl as a model is described. This protocol incorporates the use of a monoclonal antibody to biotin as the initial step in a peroxidase-based detection system. The detection of viral nucleic acid in formalin-fixed, paraffin-embedded sections using biotinylated and 35S-labelled probes is compared to the detection of viral antigen by immunocytochemistry. Biotinylated probes detected more positive cells than 35S-labelled probes and were more specific. Biotinylated probes detected more positive cells than immunocytochemistry.

In situ hybridization using biotinylated probes. An evaluation of different detection systems

In situ hybridization with biotin-labelled DNA probes is a powerful tool for the detection of viral sequences in infected tissues. However, sensitivity is low when compared to radiolabelled probes. In order to evaluate the impact on staining results of the detection system applied, we have tested various reagents. In our hands the sequential application of streptavidin and biotinylated alkaline phosphatase or development with a monoclonal anti-biotin antibody and the APAAP method gave consistently the best results. Furthermore, nitro blue tetrazolium/bromochloroindolyphosphate seems to be most suitable as a substrate for the alkaline phosphatase in this case. Use of other reagents, especially of a streptavidin-biotinylated alkaline phosphatase complex, resulted in a significantly lower staining intensity.

Localization of cytomegalovirus DNA in plastic-embedded sections by in situ hybridization. A methodologic study

The use of in situ hybridization for the identification of specific nucleic acid sequences in tissue sections has the potential for broad application in pathology. Although this technique has been successfully applied to routine paraffin sections, there have been few studies of the application of in situ hybridization to plastic-embedded tissue sections. The authors adapted techniques developed for paraffin sections to take advantage of the potential for improved morphology and more precise localization inherent in the plastic sections. A commercially available biotinylated DNA probe specific for the cytomegalovirus to develop a practical method for detection of nucleic acid sequences in plastic-embedded tissues was used. Using plastic sections, cytomegalovirus DNA sequences could readily be identified with precise localization of the virus and superb histology.

Diagnosis of progressive multifocal leucoencephalopathy by hybridisation techniques

In situ hybridisation with acetyl-aminofluorene (AAF) and 35S-labelled DNA probes for polyomaviruses, was used to detect JC virus DNA in brain necropsy material in a patient with progressive multifocal leucoencephalopathy (PML). In a second patient PML was diagnosed from a brain necropsy specimen using the same technique. The main infected cell type were oligodendrocytes; dot hybridisation was used to estimate the number of viral copies in each infected cell. Southern blot hybridisation for further analysis of the viral genome was also carried out. In situ hybridisation with non-radioactive labelled polyomavirus DNA provides a simple and specific means for studying viral DNA in formaldehyde fixed tissue sections from patients with suspected PML. Even in small biopsy samples hybridisation results can be correlated with standard histopathological, immunocytochemical, and electron microscopic findings.

JC virus genomes in progressive multifocal leukoencephalopathy: detection using a sensitive non-radioisotopic in situ hybridization method

JC virus genomes have been localized in formalin-fixed, paraffin-embedded brain tissues of two cases of known progressive multifocal leukoencephalopathy by in situ hybridization utilizing a biotinylated JC virus DNA probe. A three-stage immunoperoxidase system with gold-silver amplification of the diaminobenzidine substrate was used to visualize biotinylated nucleic acid hybrids. Dot-blot quantification of this visualization system indicates that subpicogramme amounts of biotinylated DNA can be detected. Optimal detection of the virus genomes in the brain tissues required a microwave irradiation step prior to hybridization. JC virus genomes were observed in the nuclei of enlarged oligodendrocytes and of some bizarre astrocytes. No other cell types were found to harbour the genomes.

Colorimetric in-situ hybridization in clinical virology: development of automated technology

Automation of in situ hybridization is an important first step toward practical implementation of the widely recognized diagnostic potential of nucleic acid hybridization. Our laboratory has concentrated its efforts towards automating colorimetric in situ hybridization on formalin-fixed paraffin-embedded tissue sections. We have capitalized upon the technology developed for the automation of immunohistochemistry (Brigati et al. 1988) and are collaborating with Fisher Scientific in modifying the Fisher Code-On Stainer to achieve successful automated in situ hybridization. Preliminary results are encouraging. We feel that the capillary gap technology has the potential to be modified to automate other hybridization assay formats such as dot and sandwich blot hybridizations. While specifically developed for colorimetric hybridization, the instrumentation is self-contained and could be safely adapted to the use of radio-labeled probes if necessary.

Comparative evaluation of non-radioactive in situ hybridization techniques for pathologic diagnosis of viral infection

We have compared the efficiency of biotinylated DNA probes and various visualization techniques with 35S-labeled DNA probes in routine paraffin sections from the pathology service; both autopsy and biopsy tissue were investigated. Probes included DNA genomic fragments from cytomegalovirus (CMV), Epstein-Barr-Virus (EBV) and human immunodeficiency virus (HIV). Methods of detection by Pathogene II kit (ENZO) and Blue Gene kit (BRL) with visualization by AEC, NBT/BCIP, Immunogold (Janssen) and autoradiography were used. The study shows most satisfactory results by applying the Blue Gene-NBT/BCIP combination followed by the Immunogold technique. Data obtained by these techniques compare well to those of using radioactive DNA probes and autoradiography.