Interphase cytogenetics using biotin and digoxigenin labelled probes: III. Increased sensitivity and flexibility for detecting HPV in cervical biopsy specimens and cell lines

Expression of p16 in squamous cell carcinoma of the mobile tongue is independent of HPV infection despite presence of the HPV-receptor syndecan-1

Background:

Tongue squamous cell carcinoma (TSCC) is increasing in incidence, especially among young patients and preferably females. Infection with human papilloma virus (HPV) has been suggested as a cause of SCC in the head and neck, and the proportion of oropharyngeal cancers caused by HPV has steadily increased.

Methods:

Samples from 109 patients with primary TSCC were analysed for the presence of HPV16 by in situ hybridisation and for expression of its surrogate marker p16 and the HPV receptor syndecan-1 by immunhistochemistry.

Results:

No evidence of HPV16 DNA was observed in the tumours, although one-third showed p16 staining. There was no difference in the expression of the primary HPV receptor, syndecan-1, between TSCC and a group of tonsil SCC.

Conclusion:

Whereas p16 is expressed in some TSCCs, HPV16 is undetectable, therefore, p16 cannot be used as a surrogate marker for high-risk HPV-infection in this tumour. Despite presence of the HPV-receptor syndecan-1 in TSCC, HPV prefers the tonsillar environment. Lack of p16 associates with worse prognosis primarily in patients aged ⩽40 years with tongue SCC. The improved prognosis seen in p16-positive TSCC can be due to induction of a senescent phenotype or an inherent radiosensitivity due to the ability of p16 to inhibit homologous recombination repair.

Determination of gene expression patterns by whole-mount in situ hybridization

Whole-mount in situ hybridization (WISH) is a reliable and specific method to study three-dimensional patterns of gene expression. A labeled nucleic acid probe anneals to a complementary target sequence and is visualized and localized in the embryo. This chapter describes a sensitive method for WISH on mouse embryos using digoxigenin-labeled RNA probes. The technique can be used for the analysis of gene expression patterns during early stages of odontogenesis and in tooth explants.

Improvement of non-radioactive in situ hybridization in human airway tissues: use of PCR-generated templates for synthesis of probes and an antibody sandwich technique for detection of hybridization

We describe the use of non-traditional methods of probe synthesis and quantification and detection of hybridization that appreciably improved non-radioactive in situ hybridization (ISH) in human airway tissue. To avoid the problems of bacterial cloning, plasmid digestion, and probe hydrolysis, we synthesised complementary RNA probes (riboprobes) for ISH from PCR-generated DNA. DNA template was produced by nested PCR incorporation of T7 and SP6 RNA polymerase promoters. We then compared the efficiency of in vitro transcription from PCR-generated template with traditional plasmid template by quantifying the relative probe fluorescence in denaturing gels. Transcription with SP6 or T7 polymerase in either orientation produced TNF riboprobes from a single PCR-generated template more efficiently than from plasmid, providing there were no primer hairpin loops. Fluorescence quantification enabled equal amounts of probe label to be used in ISH, eliminating signals from the sense probe and demonstrating that probes transcribed from PCR templates were as sensitive as hydrolyzed probe transcribed from plasmid. Detection of ISH by a conventional anti-hapten, alkaline phosphatase-based technique was found to cause tissue damage due to extended substrate incubation at high pH. We therefore developed a four-layer, avidin-biotin-peroxidase technique that afforded greater sensitivity, allowing brief substrate incubation and resulting in structural preservation of tissue.

Healing of full-thickness tears of avian supracoracoid tendons: in situ hybridization of alpha1(I) and alpha1(III) procollagen mRNA

Although clinically significant, much remains unknown about the healing of the torn rotator cuff tendon, because of unavailability of appropriate animal model. The human supraspinatus tendon faces the subacromial bursa superiorly, and the joint capsule inferiorly, while the digital flexor tendon is surrounded by the synovium. We hypothesized that the supraspinatus tendon heals by the process which is different from that observed with digital flexor tendons, in which epitenon cells migrate into the torn portion circumferentially. The avian supracoracoid tendon was adopted for this experiment because of its similarity to the human supraspinatus tendon. We developed a full-thickness tendon laceration followed by primary suture. The objective of this study was to detect localization of the responsible cells for repair of the tendon. We examined the process using histology and in situ hybridization. Starting at week 1 the peritendon cells of the bursal side proliferated and migrated into the laceration site. At week 6, the tendon stumps were continuous with new connective tissue. High-level expression of procollagen mRNA in the proliferating peritendon cells on the bursal side demonstrates to contribute to the reparative process, which progressed to the joint side. This mode of repair is different from that of the digital flexor tendon.

Single-copy gene detection using branched DNA (bDNA) in situ hybridization

We have developed a branched DNA in situ hybridization (bDNA ISH) method for detection of human papillomavirus (HPV) DNA in whole cells. Using human cervical cancer cell lines with known copies of HPV DNA, we show that the bDNA ISH method is highly sensitive, detecting as few as one or two copies of HPV DNA per cell. By modifying sample pretreatment, viral mRNA or DNA sequences can be detected using the same set of oligonucleotide probes. In experiments performed on mixed populations of cells, the bDNA ISH method is highly specific and can distinguish cells with HPV-16 from cells with HPV-18 DNA. Furthermore, we demonstrate that the bDNA ISH method provides precise localization, yielding positive signals retained within the subcellular compartments in which the target nucleic acid sequences are localized. As an effective and convenient means for nucleic acid detection, the bDNA ISH method is applicable to the detection of cancers and infectious agents. (J Histochem Cytochem 49:603-611, 2001)

Localisation of HHV-8 in AIDS related lymphadenopathy

BACKGROUND

Many lymph node abnormalities have been described in AIDS. These include opportunistic infections that sometimes result in spindle cell pseudotumours, Kaposi's sarcoma (KS), malignant lymphoma (Hodgkin's and non-Hodgkin's), and florid reactive hyperplasia. Among these, reactive hyperplasia is the most common manifestation of AIDS related lymphadenopathy.

AIM

To examine whether human herpesvirus 8 (HHV-8), the aetiological agent of KS, can be localised in AIDS related lymphadenopathy and whether its appearance in such nodes is predictive of Kaposi's sarcoma development.

METHODS

A series of human immunodeficiency virus (HIV) positive men (n = 21) with AIDS related lymphadenopathy who at the time of presentation had KS or subsequently developed KS (n = 5) were examined. The prevalence of HHV-8 was assessed in these patients using solution phase polymerase chain reaction (PCR), real time TaqMan quantitative PCR, and in cell amplification techniques (PCR in situ hybridisation (PCR-ISH) and labelled primer driven in cell amplification).

RESULTS

Using standard solution phase PCR in a nested format, only two of the 21 patients with AIDS related lymphadenopathy were positive for HHV-8. The lymph node of one of these patients contained KS lesions. Three HHV-8 positive patients were identified using TaqMan PCR (the original two positive patients and one additional patient). All of the positive patients either subsequently developed KS (n = 2) or had KS at the time of diagnosis (n = 1). Two additional patients subsequently developed KS, but were negative for HHV-8 by solution phase PCR and TaqMan PCR. Using PCR-ISH, HHV-8 amplicons were identified in some lymphoid cells (in one patient) and in spindle cells of the KS lesion in another. The positive lymphoid cells were predominantly concentrated in B cell areas of the affected lymph nodes, confirming the B cell tropism exhibited by HHV-8.

CONCLUSIONS

The presence of HHV-8 in AIDS related lymphadenopathy is predictive of KS development and probably represents seeding of HHV-8 infected B cells from the peripheral blood. These findings support a role for HHV-8 in the pathobiology of KS.

Endocrine tumors of the cervix: morphologic assessment, expression of human papillomavirus, and evaluation for loss of heterozygosity on 1p,3p, 11q, and 17p

BACKGROUND

Cervical endocrine tumors are rare lesions, with a varied diagnostic nomenclature. A recent consensus meeting proposed a standardized terminology. This study evaluated: 1) applicability of histopathologic guidelines; 2) evidence of loss of heterozygosity (LOH) at selected sites; and 3) the presence of human papillomavirus (HPV) detected by nonisotopic in situ hybridization (ISH).

METHODS

Thirty-eight cases (patient age range, 19-88 years; mean, 48 years) were retrieved. Outcome data were available for 32 patients. Classification was based on architectural and cytologic features. Tissue was available from 15 cases for LOH analysis with D3S1234(3p14), D3S1289(3p21), THRB(3p24), TP53(17p13), D1S468(1p36), and INT-2(11q13). In ten cases, tissue was analyzed by nonisotopic ISH with HPV probes for types 6/11, 16/18, and 31/33.

RESULTS

Tumors were divided into four groups: small cell carcinoma (SCC) (n=25); large cell neuroendocrine carcinoma (LCNC) (n=5); SCC with focal LCNC differentiation (n=3), and carcinoid tumor (n=5). Tumors defined as exclusively or predominantly SCC had a particularly poor prognosis, with 20 patients dead of disease (<6 years after diagnosis) and 6 alive with disease (after <3 years of follow-up). LOH at various 3p loci (3p14, 3p21, and 3p24) was observed in eight cases. One patient demonstrated LOH on 17p(TP53). Eight of ten cases assessed by ISH showed nuclear staining using a combined HPV-16/18 probe.

CONCLUSIONS

Cervical endocrine tumors are highly aggressive and can be subdivided into definable categories. LOH at 3p loci is a frequent finding, as is nuclear staining with a combined HPV-16/18 probe. LOH at 17p(TP53 locus) appears to be relatively uncommon, suggesting that p53 mutations may not be developmentally significant.

Identification of HHV8 in early Kaposi's sarcoma: implications for Kaposi's sarcoma pathogenesis

AIMS

Kaposi's sarcoma is a vascular tumour of uncertain pathogenesis possibly caused by an infectious agent, identified in high risk groups. Accumulating solution phase polymerase chain reaction (PCR) and seroepidemiological data suggest that a previously undescribed herpes DNA virus (human herpesvirus 8 (HHV8)) is the causative agent. Using a unique cohort of early Kaposi's sarcoma, the precise cell type infected with HHV8 in such lesions was identified to elucidate further the role of HHV8 in the pathobiology of Kaposi's sarcoma.

METHODS

Sixteen cases of early Kaposi's sarcoma (derived from skin and lymph node) were assessed for the presence of HHV8 using both standard solution phase PCR and TaqMan PCR to the KS330 Bam region of HHV8. In situ amplification was also performed on a selected group in an attempt to identify the candidate infected cells.

RESULTS

Using both conventional solution phase and TaqMan PCR, 87% of cases were positive. In addition, HHV8 amplicons were localised in situ to endothelial and spindle cell proliferations in early Kaposi's sarcoma. The HHV8 viral load varied from lesion to lesion.

CONCLUSIONS

The presence of HHV8 in early lesions supports a role for HHV8 in the pathogenesis of Kaposi's sarcoma. Coupled with recent seroepidemiological studies, these results suggest that HHV8 is the aetiological agent of Kaposi's sarcoma. Its precise interaction with other factors known to be involved in the development of Kaposi's sarcoma, including cytokines and anti-apoptosis genes, requires elucidation.

Intrinsic healing capacity and tearing process of torn supraspinatus tendons: in situ hybridization study of alpha 1 (I) procollagen mRNA

To determine the healing potential and healing process of torn supraspinatus tendons, in situ hybridization was used to localize cells containing alpha 1 type-I procollagen mRNA. Biopsy specimens of torn supraspinatus tendons from 19 patients with complete-thickness tears and 13 patients with incomplete-thickness tears were obtained during surgery. Four macroscopically normal supraspinatus tendons were obtained to serve as normal controls. Specimens were fixed in 10% buffered formalin and embedded in paraffin. A 22-mer oligonucleotide probe was labeled with digoxigenin and used as an in situ marker. The labeled cells were mainly composed of tenocytes and undifferentiated mesenchymal cells. In complete-thickness-tears, the labeled cells at the proximal tendon-stumps in the specimens that were obtained less than 4 months after trauma were significantly more abundant than in the specimens obtained 4 months or more after trauma. However, the number of labeled cells was maintained at the torn portion even in long-standing incomplete-thickness tears. The labeled cells at the margins of concomitant intratendinous extensions of the tears were detected even in the long-standing tears. The intratendinous extensions exhibited more labeled cells than the bursal-side or joint-side layers of the tendon substance in the incomplete-thickness tears (p < 0.05). The torn supraspinatus tendon may possess an intrinsic healing capability in the intermediate and late phases of tendon healing. Incomplete-thickness tears and concomitant intratendinous extensions can continue to rupture after the initial injury.

Detection of human papillomavirus in esophageal squamous cell carcinoma

BACKGROUND

Human papillomavirus (HPV) DNA has been identified in esophageal carcinomas. However, the incidence of HPV varies significantly in different geographic locations. In the current study, neoplasms from two separate geographic regions were analyzed for the presence of HPV DNA:

METHODS

One hundred and ten esophageal squamous cell carcinomas, 83 from Beijing, China and 27 from Cincinnati, Ohio, were examined for the presence of HPV DNA: In situ hybridization and polymerase chain reaction (PCR) using both consensus primers for the HPV L1 gene and type specific primers for the E6 gene of HPV types 6, 16, and 18 were performed.

RESULTS

In situ hybridization failed to demonstrate any HPV type (6, 11, 16, 18, 31, 33, or 35) in any tumor specimen. Likewise, PCR using consensus primers for the HPV L1 gene was negative in all samples. Three of the Chinese specimens (4.29%) were positive for HPV using E6 type specific primers. One tumor contained HPV type 6 DNA, whereas the other 2 contained HPV type 16 DNA. One Cincinnati tumor (4.35%) was positive for HPV 16 by type specific primer. None of the specimens contained HPV 18 DNA.

CONCLUSIONS

The incidence of HPV DNA in esophageal carcinoma specimens from Beijing, China and Cincinnati, Ohio is similar. The incidence of HPV in tumors from Beijing is significantly lower than that reported for those from other regions of China where the incidence of esophageal cancer is higher. Thus, although HPV may play a role in esophageal carcinogenesis, this role may be more pronounced in those regions of the world with a high incidence of the disease, and may be less important in areas with moderate or low risks for esophageal cancer.

Specific detection of deleted mitochondrial DNA by in situ hybridization using a chimera probe

We report a new method for the specific detection of the mutant mitochondrial DNA (mtDNA) that contains the 4977-bp deletion. We designed an oligonucleotide probe that was designated the 'ATP8/ND5 Chimera' probe: its 5'- and 3'-portions correspond to the ATP8 gene and the ND5 gene, respectively, and its middle portion includes the 13-bp direct repeat sequence that flanks the 4977-bp deletion. By Southern blot analysis, this chimeric probe specifically detected the deleted mtDNA, even in the presence of both normal mtDNA and other mtDNA deletions. The specificity of the probe was further confirmed by in situ hybridization of muscle fibers from patients with Kearns-Sayer syndrome who carry the deleted DNA in the heteroplasmic state. The deleted mtDNA was markedly accumulated in cytochrome-c oxidase (COX)-deficient ragged-red fibers. In tissues where multiple deleted mtDNAs were detected, such as muscle tissues from a patient with myotonic dystrophy and from an aged individual, the in situ hybridization detected a small number of muscle fibers that contained the deleted mtDNA. These results indicate that in situ hybridization using this chimera probe is a useful and specific method for detecting a small amount of deleted mtDNA.

Detection of human papillomavirus in esophageal squamous cell carcinoma

BACKGROUND

Human papillomavirus (HPV) DNA has been identified in esophageal carcinomas. However, the incidence of HPV varies significantly in different geographic locations. In the current study, neoplasms from two separate geographic regions were analyzed for the presence of HPV DNA:

METHODS

One hundred and ten esophageal squamous cell carcinomas, 83 from Beijing, China and 27 from Cincinnati, Ohio, were examined for the presence of HPV DNA: In situ hybridization and polymerase chain reaction (PCR) using both consensus primers for the HPV L1 gene and type specific primers for the E6 gene of HPV types 6, 16, and 18 were performed.

RESULTS

In situ hybridization failed to demonstrate any HPV type (6, 11, 16, 18, 31, 33, or 35) in any tumor specimen. Likewise, PCR using consensus primers for the HPV L1 gene was negative in all samples. Three of the Chinese specimens (4.29%) were positive for HPV using E6 type specific primers. One tumor contained HPV type 6 DNA, whereas the other 2 contained HPV type 16 DNA. One Cincinnati tumor (4.35%) was positive for HPV 16 by type specific primer. None of the specimens contained HPV 18 DNA.

CONCLUSIONS

The incidence of HPV DNA in esophageal carcinoma specimens from Beijing, China and Cincinnati, Ohio is similar. The incidence of HPV in tumors from Beijing is significantly lower than that reported for those from other regions of China where the incidence of esophageal cancer is higher. Thus, although HPV may play a role in esophageal carcinogenesis, this role may be more pronounced in those regions of the world with a high incidence of the disease, and may be less important in areas with moderate or low risks for esophageal cancer.

HPV testing in patients with low grade cervical cytological abnormalities: a follow up study

AIM

To assess the diagnostic performance of human papillomavirus (HPV) analysis in predicting cervical intraepithelial neoplasia (CIN) grades 2 and 3 in patients with persistent low grade cervical cytological abnormalities.

METHODS

Cervical smears from 167 women referred for colposcopy with persistent borderline, wart virus or mildly dyskaryotic changes on cervical screening were analysed by Papanicolaou staining, non-isotopic in situ hybridisation and generic and type specific polymerase chain reaction (PCR) amplification of HPV sequences. Follow up was by cytological and, where appropriate, histological analysis.

RESULTS

CIN grade 2 or 3 was identified in 46 patients after a median follow up of 27 months. HPV positivity by both techniques was associated with high grade CIN and with age less than 30 years (median age 33 years). Non-isotopic in situ hybridisation was more predictive but less sensitive than either generic or type specific PCR, but prediction was greater using either molecular technique in women over 30 years of age.

CONCLUSIONS

Although the degree of prediction found is of only limited clinical value, the strong association of HPV positivity with both high grade CIN and patient age suggests that further studies of HPV testing in this patient group are warranted.

cDNA cloning of an abundant human lacrimal gland mRNA encoding a novel tear protein

An abundant 1.05 kb human lacrimal gland mRNA has been characterized by cDNA cloning. It encodes a predicted 180 residue, 20546 Da secreted protein, with a charge of +11 at ph 7 and 24.5% proline, designated as Basic Proline-rich Lacrimal Protein (BPLP), Southern blot analysis is consistent with a single BPLP gene. BPLP lacks any distinct repetitive structure, and is unrelated to the salivary proline-rich protein super-family. The pre-proprotein shows modest overall similarity to a superfamily comprising human PRPb, the mouse MSG proteins, and rat VCS-alpha 1, VCS-beta 1 and submandibular apomucin. BPLP also contains a domain with similarity to the Zp2 protein domain found in several otherwise unrelated proteins. Northern blot analysis indicated that the BPLP gene is also expressed at modest levels in the human submandibular gland, and in situ hybridization demonstrated expression of BPLP in the secretory endpieces of the human lacrimal gland. The BPLP cDNA clone defines a new human tear protein, and should provide a useful phenotypic marker of differentiation in in vitro studies of lacrimal gland function.

Kaposi's sarcoma-associated herpesvirus infects endothelial and spindle cells

Kaposi's sarcoma (KS), a vascular tumour that contains characteristic spindle cells forming slit-like spaces, may have an infectious aetiology. Recently, sequences of a new human herpesvirus, KSHV/HHV-8, have been identified in both HIV-associated and classical KS. We sought to identify the target cell of this virus in KS tumour tissue. Using PCR in situ hybridization (PCR-ISH) we show that KSHV/HHV-8 is present in the flat endothelial cells lining vascular spaces of KS lesions as well as in typical KS spindle cells. These findings show that KSHV/HHV-8 is present in the cell types thought to represent neoplastic cells in these lesions.

Human papillomaviruses (HPV) in gynaecological cytology: from molecular biology to clinical testing

Molecular epidemiological and pathological studies show that different HPV types are associated with different cervical lesions allowing classification of the viruses into types associated with 'high', 'intermediate' and 'low' risk of cervical neoplasia. However, HPV infection often regresses and, where it is associated with neoplasia, is an early event. This suggests that other factors are involved in the carcinogenic process, and there is some mechanistic basis for the interaction of epidemiologically defined factors with HPV infection in the process of cervical carcinogenesis. With the refinement of techniques for HPV detection in clinical material, HPV testing is now a realistic possibility, but how this should be performed and in what clinical situation(s) is still uncertain. Particular areas of interest are: (i) the assessment of patients with borderline cytological changes or mild dyskaryosis; and (ii) the definition of those patients at greater risk of invasive disease. Clinical trials are needed before the utility of HPV testing can be properly assessed.

The detection of the mRNAs of procollagen types I, II and III in human fetal fingers by in situ hybridization using digoxigenin-labelled oligonucleotide probes

Messenger RNAs (mRNAs) encoding procollagen alpha 1 type I,alpha 1 type II and alpha 1 type III have been localized in paraffin sections of human fetal fingers using digoxigenin-labelled synthetic oligonucleotide probes. The probe-mRNA hybrids were visualized using an anti-digoxin antibody amplified with sandwich techniques. These protocols provided an excellent hybridization signal with minimal background noise. The sensitivity of the protocols was nearly equivalent to that seen when using isotopic cDNA probes. In human fetal fingers, intense hybridization signals for procollagen alpha 1 type I mRNA were detected in the osteoblasts and the fibroblasts of periosteum and perichondrium, the tenocytes of tendons, fibroblasts of ligaments, the synovial membrane and deeper layers of the dermis. In contrast, positive hybridization signals for procollagen alpha 1 type II mRNA were visualized in chondrocytes and the cambial layer of perichondrium. The signals for procollagen alpha 1 type III mRNA were detected in the fibroblasts of the dermis and perichondrium. The probes which have lower melting temperatures (Tm) could not detect the corresponding mRNAs.

Squamous intraepithelial neoplasia in an ovarian cyst, cervical intraepithelial neoplasia, and human papillomavirus

A case of squamous intraepithelial neoplasia in an ovarian cyst in association with cervical intraepithelial neoplasia (CIN) III is described. In view of the association of human papillomavirus (HPV) and CIN, the possibility that HPV infection could be associated with similar changes in the ovary was postulated. The HPV genome was shown in formalin-fixed tissue of the cervical lesion by nonisotopic in situ hybridization (NISH) and by the polymerase chain reaction (PCR). However, HPV could not be shown in the ovarian lesion by NISH or PCR. On the basis of these findings there appears to be no association between HPV infection and squamous intraepithelial neoplasia in an ovarian cyst.

Human papillomavirus DNA in oesophageal carcinomas in South Africa

Using morphological criteria, the presence of human papillomavirus (HPV) in oesophageal carcinomas has been inferred in patients from Finland and South Africa. However, studies to demonstrate the viral antigen in tissue sections of these tumours have proved disappointing. This study investigates 48 archival oesophageal carcinoma biopsies from South Africa for the presence of HPV DNA using non-isotopic in situ hybridization (NISH) with HPV DNA probes to HPV 6, 11, 16, 18, 31, and 33. HPV DNA sequences were detected in 25/48 (52 per cent) oesophageal cancers. HPV 16 was present in 84 per cent of the HPV-positive cancers. A NISH type 2 signal pattern (punctate/dot) was present in all HPV-positive tumours. This signal pattern was previously shown to represent integrated HPV DNA within host chromosome. Integrated HPV DNA in oesophageal cancers has also been demonstrated in patients from China and Japan. In addition, the prevalence of HPV DNA in oesophageal cancers from high-risk countries like South Africa (52 per cent) and China (49 per cent) would appear to be consistent.

Human papillomavirus status in the prediction of high-grade cervical intraepithelial neoplasia in patients with persistent low-grade cervical cytological abnormalities

The role of human papillomavirus (HPV) detection in the management of patients with persistent low-grade (mild dyskaryosis or less) cervical cytological abnormalities is unclear. We have analysed cytological material from 167 such patients both cytologically and by non-isotopic in situ hybridisation (NISH) for HPV 16, 18, 31 and 33 and consensus primer polymerase chain reaction (PCR) amplification followed by both generic and specific typing for these HPV types. Cervical intraepithelial neoplasia (CIN) 2 or 3 was present in 40 of 167 patients (23.9%), and the positive predictive values (PPVs) for the presence of CIN 2 or 3, of moderate or severe dyskaryosis at repeat cytology and an HPV-positive NISH and generic PCR signal were 100%, 66% and 42% respectively. The corresponding sensitivities were 48%, 68% and 87%. Addition of cytology to molecular analysis improved both PPV and sensitivity, the best combination being NISH and cytopathology (PPV 71%, sensitivity 87%). These data demonstrate that the presence of CIN 2 or 3 in patients with mild cytological abnormalities can be predicted by molecular detection of HPV in some cases, particularly when combined with cytological analysis. However, the magnitude of this prediction is dependent on the population of patients studied, and the clinical role of this approach therefore remains to be defined.

In situ hybridization in neuropathology

In situ hybridization (ISH) allows the demonstration and localization of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) in tissue sections, cells and chromosomes by utilizing a specific interaction with a labelled nucleotide probe of known composition. Although this technique has been employed for many years using radiolabelled probes, the recent development of nonisotopic labelling systems and the greatly increased availability of synthetic nucleic acids has allowed an enormous expansion in the potential applications of ISH. The technique is now applicable to unfixed and fixed tissues, including archival material. The use of enzyme-linked antibody techniques to detect labelled probes has greatly increased the sensitivity of non-isotopic ISH without a loss of specificity. The successful use of ISH demands careful selection of labelled probes, adequate tissue pretreatment to allow access of the probe, control of the stringency of probe binding and a sensitive reporter system, in addition to adequate controls. The accurate localization of nucleotides in the central nervous system (CNS) has many current research applications in the study of gene expression in multiple sclerosis and other inflammatory disorders, and a wide range of neurodegenerative disorders, viral infections and neoplasms. The technique is of diagnostic value in viral disorders, particularly where multiple infections occur. The combination of non-isotopic ISH with immunocytochemistry electron microscopy and quantitative image analysis greatly increases its research potential, while the development of a related method, the in situ polymerase chain reaction, offers an additional opportunity for further enhancing the sensitivity of this technique.

PCR in situ hybridisation detection of HPV 16 in fixed CaSki and fixed SiHa cell lines

AIMS

To investigate the feasibility of using fixed cells with the polymerase chain reaction (PCR) in situ hybridisation and to investigate possible reasons for reaction failure.

METHODS

Fixed SiHa and CaSki cells were used in an experimental model of PCR in situ hybridisation for the detection of low and intermediate copy number viral infection in fixed cells.

RESULTS

PCR in situ hybridisation was able to detect one to two copies of human papillomavirus (HPV) 16 in SiHa cells, using small fragment amplicons (120 base pairs), confirming the high detection sensitivity and flexibility of the technique. Problems were encountered with localisation of PCR amplified product in CaSki cells (200-300 copies of HPV 16 per cell) owing to diffusion of product post amplification. Overall, 40% of reactions were successful, which confirms the current unreliability of the technique. Within cell preparations, about 50% of cells contained amplified product.

CONCLUSION

PCR in situ hybridisation represents the marriage of two revolutionary molecular pathological techniques. However, it is currently unreliable, with reaction failure common. Standardised, dedicated equipment is urgently required if the technique is to achieve universal acceptance. In the future, the technique may be used to detect chromosomal translocations in human tumours and to study cellular gene expression.

Detection of Epstein-Barr virus small RNAs in routine paraffin sections using non-isotopic RNA/RNA in situ hybridization

The Epstein-Barr virus (EBV) is associated with an increasing range of reactive and neoplastic lesions. There is a need for a sensitive and specific method for detecting latent EBV in routine histological sections. We report the use of a highly sensitive paraffin section RNA/RNA in situ hybridization (ISH) technique using digoxigenin-labelled antisense riboprobes for demonstrating EBV encoded small RNAs (EBERs), EBV gene products that are transcribed in abundance during latent EBV infection. We applied EBER-ISH to 846 paraffin embedded specimens, including cases of reactive lymphoid hyperplasia (n = 28), infectious mononucleosis (16), Burkitt's lymphoma (44), immunodeficiency-associated lymphomas in transplant recipients (9) and AIDS patients (128), Hodgkin's disease (130), CD30 antigen positive lymphomas (106), peripheral T-cell lymphomas (104), sporadic B-cell non-Hodgkin's lymphomas (162), undifferentiated nasopharyngeal carcinoma (86), salivary gland lymphoepithelioma (11), and oral hairy leukoplakia (5). Strong, reproducible EBER staining was seen in EBV latently infected cells in archival surgical biopsy and autopsy specimens. EBER-ISH is specific, has a sensitivity comparable to that of the polymerase chain reaction, and is now the method of choice for the in situ detection of latent EBV infection.

Discrimination of closely homologous human genomic and viral sequences in cells and tissues: further characterization of Tmt

The experimentally derived parameter Tmt (tissue Tm) was defined previously to describe the end-point used for evaluation of the stringency of non-isotopic in situ hybridization and was found to differ from the theoretical melting temperature (Tm) for several HPV types. In this paper, the reasons for this discrepancy were investigated by performing a series of experiments with a variety of probes for both human genomic and integrated viral sequences in isolated and cultured normal and abnormal cells in addition to paraffin-embedded material. Tmt was shown to be dependent on several parameters of probe and target, and on the sensitivity of the detection system used but was not affected by aldehyde fixation or paraffin wax embedding under optimal conditions of nucleic acid unmasking. These data support the hypothesis that differences between Tmt and Tm may be due to the use of a different end-point for in situ hybridization analysis rather than biochemical alteration of DNA-DNA interactions in intact cells. Appropriate stringency conditions should therefore be determined by experiment rather than calculated theoretically for gene evaluation in cells and tissues.

Squamous cell papillomas of the esophagus: a study of 23 lesions for human papillomavirus by in situ hybridization and the polymerase chain reaction

This study assessed squamous cell papillomas of the human esophagus for the presence of human papillomavirus (HPV) and correlated the results with histological features. Twenty-three lesions obtained by endoscopic biopsy from 17 patients were studied, first by in situ hybridization (ISH) for HPV types 6-11, 16-18, 18, and 31-33-51, and second by the polymerase chain reaction (PCR) with amplification of multiple HPV types and demonstration of amplified product by ethidium bromide staining and Southern blot hybridization for HPV types 6-11, 16, and 18 in each case. Evidence of HPV DNA was found in only one lesion, which showed HPV type 6-11 by ISH and HPV positivity by Southern blotting of the amplified product after the PCR. This case exhibited histological features suggestive of HPV infection, although no morphological changes specific to the lesion were identified. The remaining 22 lesions, including those from cases in which multiple papillomas were present, were negative for HPV. The results show that HPV DNA is frequently not detectable in esophageal squamous cell papillomas, even when highly sensitive techniques are used. These findings are consistent with the hypothesis that other pathogenetic mechanisms, such as mucosal injury and repair, are important in the etiology of these lesions.

In situ hybridization of cytospin preparations: a rapid nonisotopic screening method for isolated cells

A simple and rapid method for light microscopic in situ hybridization on cytospin preparations is described and demonstrated for detection of viral nucleic acid in a virus-infected cell line. Cells were fixed by acetone followed by chloroform, denatured by heat, hybridized at 37 C, and hybridized sites detected with a multiple step procedure (primary anti-biotin antibody, biotinylated second antibody, streptavidin-peroxidase). This method can be used for screening studies at the light microscope level, and offers a useful and simple way to determine optimum hybridization conditions for subsequent electron microscopic investigations.

Non-isotopic in situ detection of mRNA for interleukin-4 in archival human tissue

Non-isotopic in situ hybridisation (NISH) is a rapid and sensitive method currently used in molecular pathology to identify DNA in fresh and archival human biopsies. In this study we have extended NISH technology for mRNA detection to include the use of digoxigenin-labelled riboprobes to localise low abundance mRNA for interleukin-4 in paraffin embedded material (from active inflammatory bowel disease). As this methodological approach makes the retrospective study of cytokine gene expression in archival material possible for the first time, it could act as a prototype for studies of cytokine involvement in various human diseases.

Regulation of tumor necrosis factor-alpha-mRNA synthesis and distribution of tumor necrosis factor-alpha-mRNA synthesizing cells in rat liver during experimental endotoxemia

Stimulated liver macrophages (Kupffer cells) are known to release a variety of inflammation-related substances, e.g. cytokines, prostanoids, and reactive oxygen intermediates. For instance, exposure of Kupffer cells in vitro to lipopolysaccharide (endotoxin) leads to a strongly enhanced synthesis of the mRNA for tumor necrosis factor-alpha, the release of the mature protein into culture media. These events are influenced by prostanoids and corticoid hormones. Kupffer cells are thought to be the only source of tumor necrosis factor-alpha within the hepatic sinusoid, but neither this cell specificity nor the regulatory influence of glucocorticoids or prostanoids has been confirmed in the intact organ. Using non-radioactive in situ hybridization, it was possible to obtain specific signals for tumor necrosis factor-alpha-mRNA in individual Kupffer cells uniformly distributed (as compared to Kupffer cells detected by immunohistochemistry) throughout the liver. Kupffer cells were the only cells in the hepatic sinusoids of lipopolysaccharide-perfused livers to express mRNA for tumor necrosis factor-alpha. Simultaneous addition of endotoxin plus dexamethasone and endotoxin and prostaglandin E2 completely suppressed the synthesis of this mRNA. Unexpectedly, the presence of mRNA for tumor necrosis factor-alpha was also detected in the intrahepatic bile duct epithelium of lipopolysaccharide-perfused livers. It is known that biologically active endotoxin is secreted via the bile ducts. These results seem to indicate that bile duct epithelium responds to inflammatory agents with synthesis of tumor necrosis factor-alpha-mRNA. One must also consider new functional aspects of bile duct epithelium in chronic inflammatory diseases, e.g. primary biliary cirrhosis, chronic sclerosing cholangitis or graft-versus-host disease.

p53 antigen in cervical condylomata, intraepithelial neoplasia, and carcinoma: relationship to HPV infection and integration

It has been proposed that wild-type p53 cell-regulating functions are annulled in human cervical carcinomas, either by mutations in the human papillomavirus (HPV)-negative cases or as a consequence of their complexing with HPV E6. The aim of this study was to test this hypothesis on 39 fresh cervical biopsies by p53 immunocytochemistry (ICC) with antibody PAb 240 and with NISH (non-isotopic in situ hybridization) and PCR (polymerase chain reaction) for HPV detection. p53 protein was present in the basal layer of pure wart virus infection; the basal to middle third of CIN (cervical intraepithelial neoplasia); in 19/22 (86 per cent) HPV-positive cervical carcinomas, ten of which contained integrated HPV; and in 4/8 (50 per cent) HPV-negative cervical carcinomas. Dual detection of p53 antigen and HPV 16 DNA in the same sections demonstrated either p53 protein or integrated HPV 16 alone in the majority of cells. Co-localization of both signals was only evident in isolated cells. These data suggest that PAb 240 immunoreactivity is not mutant-specific. They are, however, consistent with the conformation hypothesis which proposes that wild-type p53 changes from a suppressor (PAb 240-negative) to a promoter (PAb 240-positive) form during cell growth response. Hence, according to this hypothesis, p53 protein expression may represent either the wild-type promoter form or mutant p53 protein, both of which share the same conformation. This may explain co-localization of p53 and HPV in some tumours. However, the absence of p53 protein in 50 per cent HPV-negative squamous cell carcinomas suggests that not all HPV-negative tumours accumulate p53 protein.

The discrimination of high-risk HPV types by in situ hybridization and the polymerase chain reaction

The parameter Tmt has been defined by non-isotopic in situ hybridization and describes the tissue melting temperature (Tmt) of human papillomavirus (HPV) DNA sequences. In this study, multiple in situ hybridization signals for HPV types 16, 31 and 33 in individual archival biopsies hybridized with genomic probes are shown by polymerase chain reactions to be due to cross-hybridization of probe sequences to a single tissue target. Tmt is independent of viral type but depends on the homology between probe and target when using nick-translated whole genomic probes. The difference between Tm and Tmt is not due to the presence of viral capsid protein. Multiple HPV signals in archival material should not therefore be interpreted as indicative of multiple HPV infection unless adequate stringency conditions have been employed or they are present in morphologically distinct areas of the biopsy. Furthermore, extrapolation of calculated DNA homologies to non-isotopic in situ hybridization analysis may not be appropriate. A hybridization signal does not imply probe and target identity: this has implications for HPV typing in clinical material.

In situ detection of human Ig light-chain mRNA on formalin-fixed and paraffin-embedded tissue sections using digoxigenin-labelled RNA probes

Digoxigenin-labelled RNA probes complementary to human immunoglobulin (Ig) kappa and lambda light-chain mRNAs were produced by in vitro transcription. Using these probes, several existing in situ hybridization protocols were studied. By modifying and optimizing pretreatment procedures, which include hybridization, stringency washings and probe detection, a simplified non-radioactive in situ hybridization method for Ig light-chain mRNAs was developed. The light-chain signals were consistently identified in plasma cells, germinal centrocytes, centroblasts and immunoblasts in formalin-fixed and paraffin-embedded sections of lymphoid tissues. Monotypic light-chain mRNA was demonstrated in archival cases of kappa or lambda light-chain-restricted B-cell lymphoma. Background staining was found to be negligible in all the tissues tested. These results indicate that the in situ hybridization methodology described in this study is specific and sensitive for the detection of Ig light-chain mRNAs and has practical value in routine histology.

Influence of fixation on human papillomavirus DNA detection in frozen and embedded paraffin lesions by in situ hybridization with biotinylated probes

Series of frozen or paraffin-embedded tissues from various body sites, taken from non-immunosuppressed or immunosuppressed patients with persistent papilloma lesions were examined for the presence of group specific antigen from human papillomavirus (HPV) by indirect immunofluorescence or HPV DNA by in situ hybridization with biotinylated probes. We have shown that it is possible to detect HPV DNA after fixation of tissues in neutral formalin, Bouin's or Baker's solution. However, the sensitivity was reduced as compared to frozen tissues. The HPV DNA was detected in nuclei of heavily infected epithelial cells such as plantar or hand warts or in dispersed cells containing high copy numbers of HPV DNA from lesions such as squamous cell carcinomas or keratoacanthomas. In premalignant or malignant lesions of both immunosuppressed or non-immunosuppressed patients, HPV DNA was rarely detected after fixation. HPV types commonly described for skin and genital samples were identified in non-immunosuppressed patients, whereas in transplant recipients oncogenic HPV type 16 was identified in benign warts as well as in premalignant or malignant lesions. Positive reactions with several HPV types were more frequent in lesions from grafted patients than from the normal population. Virus antigen was detectable more frequently in frozen sections than in fixed tissues. Our findings indicate that in situ hybridization is an appropriate and rapid technique to study the presence of HPV infection. However, numerous controls are needed to avoid misinterpretations.

Integration of human papillomavirus types 16 and 18 in cervical adenocarcinoma

AIMS

To determine which type of human papillomavirus (HPV) is associated with cervical adenocarcinoma and whether the virus was integrated or episomal in two continents.

METHODS

Biopsy specimens from the UK (n = 16) and South Africa (n = 22) were analysed by non-isotopic in situ hybridisation (NISH) for HPV types 6, 11, 16, 18, 31, 33, and 35 on archival biopsy specimens using digoxigenin labelled probes.

RESULTS

A total of 20 adenocarcinomas (53%) from both groups contained HPV DNA. In the UK group, seven and four cases contained HPV 18 (44%) and 16 (25%) respectively. In the South African group, nine cases contained HPV 18 (41%) while HPV DNA was not detectable in the other 13 cases. Hence HPV 18 was present in 80% of HPV positive adenocarcinomas.

CONCLUSIONS

The HPV 16 or 18 genome was integrated in all viral positive cases. In two cases HPV 18 was also present in an episomal form. These data indicate that HPV integration is common to cervical adenocarcinoma in two continents by the same methodology. The lower prevalence of HPV 18 detection in the South African group may have been due to the presence of other or unsequenced HPV types.

Comparison of four in situ hybridization methods, based on digoxigenin- and biotin-labelled probes, in detecting HPV DNA in male condylomata acuminata

We have compared the efficacy of digoxigenin- and biotin-labelled probes in detecting HPV DNA by in situ hybridization on paraffin-embedded tissue sections of 57 male condyloma-suspect genital lesions. Each biopsy was hybridized with at least three of the following four methods: digoxigenin-labelled HPV DNA probes (Dig-HPV), biotinylated HPV-DNA probes (Bio-HPV), and two commercial methods (ViraType in situ and PathoGene), both based on biotinylated DNA probes. The hybridization products were visualized with colourigenic enzyme substrates. In most biopsies, the 4 methods gave equal results although cross-hybridization was most often found with the low-stringency ViraType method. Dig-HPV 6/11 probes gave positive results about twice as often as either of the commercial methods. No such difference, however, was found for HPV 16/18 probes. DNA of any type of HPV 6/11, 16/18 or 31/33/35 or 51 was detected in 28/43 (65%) of lesions showing condyloma acuminatum histology but in none of the 14 biopsies with no histological signs of HPV infection. In HPV-positive condylomata with no cellular atypia. HPV 6/11 was detected in 87% (13/15), and HPV 16/18 in 27% (4/15). In biopsies with cellular atypia, HPV types 6/11 were detected in 62% (8/13), HPV types 16/18 in 46% (6/13), and HPV types 31/33/35 or 51 in 50% (6/12). In about 50% of the biopsies where at least one hybridization method gave a positive result, either one of the commercial methods gave a negative result.(ABSTRACT TRUNCATED AT 250 WORDS)

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.

Episomal and integrated human papillomavirus in cervical neoplasia shown by non-isotopic in situ hybridisation

It was postulated that non-isotopic in situ hybridisation (NISH) signal types 1-3 for human papillomavirus in cervical biopsy specimens represent episomal or integrated virus. The aim of this study was to validate this hypothesis by independent molecular techniques. Fresh cervical intraepithelial neoplasia (CIN) and squamous cell cancer (SCC) tissue were examined for NISH signal pattern by hybridising with digoxigenin labelled HPV 16. DNA was extracted from the same samples and analysed by restriction endonuclease digestion and Southern blotting to determine the physical state of the viral genome. Six CIN biopsy specimens showed a type 1 NISH signal for HPV 16. On Southern analysis these biopsy specimens contained only episomal HPV 16. Three SCC with a type 2 NISH signal contained integrated HPV 16 by Southern analysis. Two specimens, a CIN 3 and an SCC with a type 3 NISH signal for HPV 16, showed the presence of both episomal and integrated HPV 16 with conventional Southern analysis and two dimensional gel electrophoresis. These results show that episomal HPV can be reliably determined by NISH type 1 signal, integrated HPV by type 2, and a combination of both episomal and integrated HPV, by a type 3 signal in archival paraffin wax embedded cervical biopsy specimens. This will add another variable to the epidemiological studies of HPV infection. In particular, it will now allow retrospective studies to be done to define the role of episomal and integrated HPV in the evolution of cervical intraepithelial neoplasia and other cervical disease associated with this virus.

Ultrastructural visualization of human papillomavirus DNA in verrucous and precancerous squamous lesions

Human papillomavirus (HPV) DNA was ultrastructurally localized by the non-isotopic in situ hybridization technique in formalin-fixed, paraffin-embedded specimens of verruca vulgaris of the skin, condyloma acuminatum of the penis and severe dysplasia of the uterine cervix. Biotinylated DNA probe cocktails were employed for the visualization of HPV-DNA, types 6 and 11 (HPV 6/11) and types 16 and 18 (HPV 16/18). The papillomavirus genus-specific antigen was also visualized by pre-embedding immunoelectron microscopy using rabbit antiserum. In verruca vulgaris, HPV antigen-positive 50-60 nm-particles of mature viral size were observed in the nuclei of the granular cells and parakeratotic cells with perinuclear haloes, whereas HPV 6/11 and HPV 16/18 DNA were negative. In condyloma acuminatum, the nuclei were positive for the HPV antigen and HPV 6/11 DNA, but were negative for HPV 16/18 DNA. More cells were labeled for the viral DNA than for the viral antigen. The ultrastructural observation indicated the presence of the naked (plasmid) viral DNA as fine particles sized 15-20 nm. In the dysplastic cervical mucosa, dot-like positivity of HPV 16/18 DNA was recognized. The HPV antigen and HPV 6/11 DNA were undetectable. HPV 16/18 DNA was localized in part of the nuclear chromatin. This pattern of localization may suggest integration of the viral DNA into the host cell DNA.

Model system for optimising mRNA non-isotopic in situ hybridisation: riboprobe detection of lysozyme mRNA in archival gut biopsy specimens

The aim of this study was to optimise conditions for mRNA detection by nonisotopic in situ hybridisation (NISH) using biotinylated and digoxigenin labelled riboprobes. Because lysozyme gene transcripts are present at high concentrations in Paneth and other alimentary cells, archival gut biopsy specimens were chosen as a model system for these experiments. Most of the variables in NISH, from unmasking of mRNA, to its ultimate detection by peroxidase or alkaline phosphatase based detection systems, were examined in detail. The most important findings were that simultaneous heating of tissue targets and riboprobes at 95 degrees C for 15 minutes before hybridisation at 50 degrees C for two hours gave the most intense signal for lysozyme mRNA in Paneth cells, Brunner's glands, and lamina propria macrophages; digoxigenin labelled riboprobes gave a higher signal to noise ratio than their biotinylated counterparts, and probes 600 base pairs long were superior to shorter probes. It is concluded that the mRNA NISH method may be generally useful for detecting gene transcription in archival clinical biopsy specimens.