WO2008079987A2

WO2008079987A2 - Detection of transcripts

Info

Publication number: WO2008079987A2
Application number: PCT/US2007/088391
Authority: WO
Inventors: Robert L. Bacallao; Rajesh Kher
Original assignee: Indiana University Research And Technology Corporation
Priority date: 2006-12-22
Filing date: 2007-12-20
Publication date: 2008-07-03
Also published as: WO2008079987A3

Abstract

An improved method is provided for conducting an in situ fluorescence-based reverse transcriptase PCR method for detecting mRNA transcripts in tissue samples.

Description

DETECTION OF TRANSCRIPTS

BACKGROUND

Cervical cancer is the third most common cancer in women in the United States after skin cancer and breast cancer, respectively (1). Since its introduction in the 1940 's the Pap smear has been the standard method of cytological screening of the cervix. An estimated 50 million Pap smears are performed each year in the United States (2). A large body of evidence supports an etiologic role of human papillomavirus (HPV) in the development of cervical cancer and its intraepithelial precursor lesions (3-7). Approximately one third of the 100 known human papillomavirus (HPV) types regularly infect the genital tract, leading to a range of pathologic states include asymptomatic carriage of virus, genital warts, cervical dysplasia, and cervical carcinoma (8-11). Approximately 15% of reproductive-age women score positive for high-risk HPVs. The presence of high-risk human papillomavirus genital subtypes increases the risk of malignant transformation. Numerous individual HPV types including low-risk types are associated with cervical dysplasia and their precise role in cervical cancer pathogenesis is not precisely known (12).

The false-negative rate for screening in the general population reportedly has been as high as 20% to 30% with Papanicolaou-stained (Pap) smear screening and 1.1% to 7.5% with HPV DNA testing (13). Accordingly, an enhanced molecular test is desirable.

SUMMARY

Cellular localization of the viral DNA is useful in clinical decision making. In benign lesions caused by HPV, viral DNA is located extrachromosomally in the nucleus while in high-grade intraepithelial neoplasias and cancers, HPV DNA is generally integrated into the host genome (13). One embodiment of the present disclosure is directed to a semi-quantitative molecular test that can enable the detection and localization of viral nucleic acids. In addition, information provided by such a molecular test may be utilized to indicate the severity of disease. BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1. demonstrates the detection and localization of E1E4 mRNA in HPV infected human foreskin mouse xenografts. Panel A: HPV negative xenograft. Panel Bl : HPV infected xenograft (renal tubes). Panel B2: HPV infected xenograft (arrows indicate viral transcripts co-localized with GAPDH). Panel C: DNA In situ hybridization showing detection of HPV sequences in HPV infected xenograft (red color-CY5 represents HPV and green color-FITC represents GAPDH, the combination of staining yields a yellow color).

Figure 2. demonstrates the detection and localization of E1E4 mRNA in HPV infected foreskin mouse xenografts. Panel A: HPV negative xenograft.

Panel B: HPV infected xenograft (arrows indicate viral transcripts co-localized with GAPDH). Panel C: HPV infected xenograft (renal tubes).

Figure 3. Whole mount in situ RT-PCR of a mouse embryonic kidney. Fluorescent tagged primers specific for Tyro-3 were used in this experiment. Reaction conditions and tissue handling were as described in the Examples except that incubation times of enzyme digests and primers labeling were altered to allow complete penetration of all reagents throughout the sample. In addition wash conditions were optimized to remove background staining.

DETAILED DESCRIPTION

While the invention is susceptible to various modifications and alternative forms, specific embodiments will herein be described in detail. It should be understood, however, that there is no intent to limit the invention to the particular forms described, but on the contrary, the intention is to cover all modifications, equivalents, and alternatives falling within the spirit and scope of the invention.

Fluorescence based in situ reverse transcriptase-polymerase chain reaction (IS-RTPCR) is a quantitative, sensitive and specific technique for RNA detection and localization for pathological diagnosis of cervical cancer and other related abnormalities. The fluorescence-based method can be used to identify the sites of RNA transcript production in patient tissues. Applicants have developed an in situ reverse transcriptase PCR method in which the background fluorescence is greatly reduced as compared to traditional in situ PCR. Such a technique is disclosed in US published patent application no. 20030059801, published on March 27, 2003, the disclosure of which is fully incorporated herein by reference.

The method described herein can be used to detect transcripts of HPV genes directly on Pap smear slides. The method can be further used to detect transcripts of the transforming HPV genes, E6 and E7, directly on Pap smear slides. The method can be used to determine if the HPV genes responsible for causing malignant changes are present and transcriptionally active in the host cells. Additionally, the method allows localization of HPV in the host cells simultaneously on the same slide. Detection and analysis can be automated on fluorescent microscopes.

Elimination of genomic DNA results in higher specificity. In addition, elimination of genomic DNA reduces the chances of false-positive results that are inherent in the methods available presently (14, 15). The method described herein can be used to reliably triage the common cytological diagnoses of ASCUS (atypical squamous cells of undetermined significance) and LSIL (low-grade squamous intraepithelial lesions), which represent the bulk of cervical abnormalities seen on Pap smears. This highly sensitive method can provide physicians with an objective measurement of cervical cancer or precursor risk.

Examples: Separate primer pairs specific to transforming genes, like HPV E1E4,

E6 and E7 genes of various high and low risk HPV, were designed using Oligo 60 program or other standard primer design software. Sense primers were tagged with Cy5 at 5' end by the manufacturer at the time of synthesis. Various conditions for successful amplification by these primer sets were established by doing solution based RT-PCR assays. Specificity of the primers for amplifying E1E4, E6 and E7 transcripts of different HPV types were determined by direct sequencing of the amplicons or by sequencing of the amplified products cloned in a Zero Blunt Topo™ vector (In Vitrogen).

Pap smear samples and formalin-fixed paraffin embedded archival cervical biopsy samples were used. Pap smear samples were fixed in 4% paraformaldehyde- 15% sucrose solution overnight at 4°C and stored at -8O⁰C until processed for ISRT-PCR. The paraffin embedded samples were deparaffinized and dehydrated in graded series of ethyl alcohol.

The slides (both Pap and biopsy samples) were incubated for 10 seconds at 105-11O⁰C. Optimal conditions for protease digestion of paraformaldehyde fixed Pap smear slides and of paraformaldehyde/formalin paraformaldehyde fixed Pap smear slides and of paraformaldehyde/formalin fixed cervical biopsies were determined. Insufficient digestion with proteinase K will not permit restriction enzymes and DNAsel access to the genomic DNA. Proteinase K digestion conditions were standardized by performing digestions in graded concentrations of the enzyme for a fixed time at 37⁰C. The highest concentration of the enzyme that did not change the cytoarchitecture of the cells was used. Appearance of salt and pepper dots was an indication of optimal digestion. At that stage the digestion was stopped by incubating the slides for 2 minutes at 110° C. Further optimization of digestion was undertaken by digesting different samples each with the above fixed concentration of proteinase K at 37⁰C for varying time periods. The digestions were stopped at 110°C for 2 minutes. This was followed by doing an in situ PCR with any housekeeping primers like GAPDH or /3-Actin. The digestion time that gives the strongest signal in maximum number of nuclei is the optimal digestion time. A duplicate slide of the same sample as used above was subjected to restriction enzyme digestion for 3 hours with a specific tetra cutter enzyme (i.e. a restriction endonuclease that has a recognition sequence consisting of 4 nucleotides) under recommended conditions of digestion. The digestion was carried out in a humidified chamber. After restriction digestion the samples were subjected to overnight DNAse I digestion in the presence of RNAsin in a humidified chamber. After overnight DNAse I digestion the sample was subjected to in situ PCR with GAPDH or β-Actin primers as before. The complete elimination of signal confirms the optimal protease digestion conditions for that sample.

After the standardization of enzyme digestions, in situ RT reaction followed by in situ PCR was carried out as per the standardized protocol (16). In situ RT-PCR was followed by counterstaining the samples with hematoxylin for determination of sub-cellular localization of the amplified viral transcripts. Samples were imaged with a Zeiss LSM 510 confocal equipped with Ar and He/Ne lasers. Samples were excited at 633 run and images collected with a 650 nm emission filter in the light path. All images were collected using standardized laser intensities and photomultiplier tube settings for amplification and dark levels. All images were processed with Adobe Photoshop. Quantitation of Cy5 fluorescence was performed with Metamorph. A scoring method was developed for densitometeric analysis of the amplified fluorescent gene products that can be used for correlation of viral load with severity of the disease.

Cellular localization of HPV E1E4 mRNA along with GAPDH simultaneously with direct in situ reverse transcriptase-polymerase chain reaction

The fluorescence-based method of in situ RT-PCR is highly specific, allowing the identification of RNA transcript production in tissues. With this method, direct detection of the transcripts of transforming genes, e.g., E1E4, E6 and E7 of HPV can be performed on Pap smear slides. This technique allows the determination that transcripts of the HPV genes responsible for causing malignant changes are present and are transcriptionally active. This method also allows the localization of different HPV genes in the host cell simultaneously on the same slide.

Figure 1 demonstrates that detection of two genes can be accomplished using two different fluorotags in fluorescence-based in situ RT PCR. As demonstrated by the results, shown in Figure 1 , the present method successfully detected and localized the expression of HPV E1E4 mRNA and GAPDH mRNA. Foreskin xenografts were obtained from infectivity experiments using HPV virus. Foreskin xenografts were first infected with HPV and then embedded in the renal capsule. These samples were fixed and paraffin embedded and then sectioned. Paraffin embedded tissue sections were deparaffinized, dehydrated and rehydrated in graded alcohol series as per standard protocols. The cells were permeabilized with Proteinase K and IS-RTPCR was carried out with primers specific for HPV E1E4 and GAPDH. The samples were imaged with a Zeiss LSM 510 confocal microscope equipped with Ar and He/Ne lasers. The images were processed with Adobe Photoshop.

The present method can be used to simultaneously detect two or more genes in a single tissue sample. To conduct multiple gene detection by in situ RT PCR, the tissue sample is contacted with a first and second set of PCR primers wherein the first and second set of PCR primers specifically bind and amplify two different genes, and at least one of the first set of PCR primers is labeled with a first fluorophore and at least one of the second set of PCR primers is labeled with a second fluorophore, wherein the emission spectra of the first fluorophore and the second fluorophore are separately detectable when both are present. For example, in order to demonstrate two color gene detection, the E1E4 forward primer was tagged with cy5 at the 5' end while a GAPDH forward primer was tagged with FITC at the 5' end. Both the reverse primers were unlabeled. Various conditions for successful amplification by these primer sets were established by doing solution based RT-PCR assays. Specificity of the primers for amplifying E1E4 transcripts of different HPV types were determined by direct sequencing of the amplicons or by sequencing of the amplified products cloned in a Zero Blunt Topo™ vector (In Vitrogen).

Figure 1 shows the detection of two genes using different fluorotags in fluorescence-based in situ RT-PCR. In addition, figure 1 shows the detection and localization of the expression of HPV E1E4 mRNA and GAPDH mRNA. Panel A is an HPV negative xenograft showing localization of GAPDH but no viral transcripts. HPV E1E4 mRNA expression was detected in foreskin xenografts. Panel Bl is an

HPV infected xenograft showing GAPDH localization in the renal tubules which were uninfected. No viral localization was detected in this region. Panel B2 is an HPV infected xenograft showing viral transcripts (arrows) co-localized with GAPDH (different region of slide from Panel Bl). Panel C represents DNA In situ Hybridization showing detection of HPV sequences in HPV infected xenograft (red color-CY5 for HPV and green color-FITC for GAPDH, the combination of which gives yellow color) (Slide matched with B). Two-color gene detection using fluorescence-based in situ RT PCR is shown. Correlation with known HPV copy numbers may be performed. Arrows indicate the cells containing HPV. Figure 2 shows the detection and localization of E1E4 mRNA in HPV infected foreskin mouse xenografts. Panel A is an HPV negative xenograft showing localization of GAPDH but no viral transcripts. Panel B is an HPV infected xenograft showing viral transcripts (arrows) co-localized with GAPDH. Panel C is an HPV infected xenograft (different region of slide shown in Panel B) showing GAPDH localization in the renal tubules which were uninfected. No viral localization was detected in this region. This data shows two-color gene detection using fluorescence- based in situ RT-PCR.

A duplicate slide of the same sample as used in figure 1 was subjected to restriction enzyme digestion for 3 hours with a specific terra cutter enzyme under recommended conditions of digestion. A restriction enzyme that cuts at least once within the genomic DNA region lying between the GAPDH specific PCR primers was chosen. Traces of any endogenous genomic DNA are eliminated and the RT-PCR signal is contributed unequivocally by mRNA. Total elimination of genomic DNA results in higher specificity and eliminates chances of false-positive results that are inherent in the methods available presently. Additionally, DNAse I treatment coupled with treatment with specific restriction enzymes (enzymes that cut at least once or more within the genomic region that lies between the amplification primer pairs) results in removal of any false positive signal contributed by genomic DNA. Preferably, the choice of restriction enzyme is specific to the gene(s) of interest.

DNA digestion was carried out in a humidified chamber. After restriction digestion the samples were subjected to overnight DNAse I digestion in the presence of RNAsin in a humidified chamber. After overnight DNAse I digestion, the samples were subject to in situ PCR with GAPDH or /3-Actin primers as described. The substantial elimination of signal confirms the optimal protease digestion conditions for that sample.

After the standardization of enzyme digestions, in situ reaction followed by in situ PCR was carried out as described. In situ RT-PCR was followed by counterstaining the samples with hematoxylin for determination of sub-cellular localization of the amplified viral transcripts. Samples were imaged with a Zeiss LSM 510 confocal microscope equipped with Ar and He/Ne lasers. Samples were excited at 633 nm and images collected with a 650 run emission filter in the light path. All images were collected using standardized laser intensities and photomultiplier tube settings for amplification and dark levels. All images were processed with

Adobe Photoshop. Quantitation of Cy5 fluorescence was done with Metamorph. A scoring method was developed for densitometeric analysis of the amplified fluorescent gene products that can be used for correlation of viral load with severity of the disease. Because virtually all nonspecific fluorescence is eliminated, this method can be used as a determinative tool for HPV infection as well as for visualizations of cellular abnormalities associated with the infection. Incorporation of the fluorotag in the sense primer obviates the need for a technologically demanding and tedious separate in situ hybridization step and thus makes this technique a rapid test. This molecular technique also provides physicians with a cytological tool to determine the severity of the disease by semi-quantification of the amplified viral gene transcripts. A second application of the presently disclosed method has been the use of IS-RTPCR to detect genes in thick sections or whole mount tissues. Thick sections as used herein is intended to include samples having a thickness of 50-100 micron thickness, and in one embodiment about 100 microns or greater. Figure 3 demonstrates the labeling of tyro-3 in a whole mount mouse embryonic kidney

(E15.5). This tissue is 100 micron thick. No physical method of sectioning was used to produce this image and the image is comprised of 100 optical sections taken 1 micron apart. We found that if there is any genomic contribution to the fluorescent signal in whole mount or thick sections of tissue, the resultant image is unusable. Genomic contamination can spill out of the cytoplasm space and bleed into surrounding tissue when In-Situ RT PCR is performed. When our method is scrupulously adhered to, no genomic contamination of the fluorescent signal is observed. Our method is the only one that enables fluorescent microscopy evaluation of gene expression in thick sections or whole mount tissues. This will enable us to examine the spatial distribution of gene expression in thick sections.

The importance of this development is in molecular diagnostics of tumors. For example in pathological analysis of breast masses, excised masses are fixed and then a small sample of the tissue is used for pathological analysis. Typically 10 tissue sections are examined, each section is 5-10 microns thick. For a 1 cm mass, this means that less than 10% of the mass is examined. With our technology, gene expression could be examined in 10 100 micron thick sections giving 100% coverage of the tumor. In addition, gene expression within the context of cellular niches could be determined.

Fixation: Pap smear samples and formalin-fixed paraffin embedded archival cervical biopsy samples were fixed in 4% paraformaldehyde- 15% sucrose solution overnight at 4° C and stored at -80° C until processed for ISRT-PCR. The paraffin embedded samples were deparaffinized and dehydrated in graded series of ethyl alcohol.

Processing: Prior to Proteinase K digestion, slides were incubated for 10 seconds at 105° C on a heat block to ensure tissue adhesion to the slides. The slides were then immersed at room temperature for 27 minutes in Proteinase K solution at a final concentration of 6.66 μg/ml. Digestion conditions were standardized by performing digestions in graded concentrations of Proteinase K for a fixed time. Enzyme digestions were stopped by incubating the slide for 2 min. at 110° C on a heat block. Samples were rinsed briefly, first in PBS and subsequently in DEPC treated water. The slides were air-dried.

After Proteinase K treatment, the genomic DNA in each sample was digested in situ using a humidified chamber at 37° C for 3 hours with 10-20 unites of Sau96I alone or in combination with a tetra-cutter enzyme (e.g., Hae III or Hpa II) in universal buffer containing 10 U of RNAsin in a total volume of 20 μl. The slides were washed for 10 seconds each in PBS and DEPC-water. To ensure complete digestion of genomic DNA in the tissue sections, samples were incubated overnight in a humidified chamber at 37° C with 10 U of RNase-free DNAse (1 U/μl final concentration). The slides were then rinsed twice for 10 seconds each with DEPC treated water.

In situ reverse transcriptase reaction: The slides were overlaid with 10 μl of RT mix, Ix 1^st Strand Buffer (Gibco-BRL, Rockville, MD), 1 mN each of dATP, dCTP, dGTP and dTTP, 10 U of RNAsin, 6mM DTT, 0.5 μM of 3'-primer (unlabeled primer for equimolar amounts of 3' primers for EIE4 HPV and GAPDH combined) and 5 U of Superscript II RT enzyme (Invitrogen) and incubated at 42° C in a humidified chamber for 1 hour. Reverse transcriptase was omitted from the RT mix for RT minus control slides. Reverse transcription reaction was stopped by incubating the slides for 2 min. at 92° C in a MJR PTC-100 thermal cycler (MJ Research, Watertown, MA) fitted with a slide holder. The cover slips were removed and samples washed twice with DEPC-water.

In situ polymerase chain reaction: For amplification of the target E1E4 HPV and/or GAPDH sequences, PCR was carried out in situ on the slides using MJR's PTC-100 thermal cycler. 5' primers of E1E4 HPV and GAPDH were labeled separately with cy5 and FITC and were included in the PCR reaction in equimolar amounts. Slides were kept at 4° C prior to the start of the PCR reaction. 10-20 μl of PCR mix was overlaid on the sections and the slide was sealed with adhesive cover slips (Sigma, St. Louis, MO). reactions were performed in the presence of Ix GeneAmp PCR Buffer containing 1.5 mN MgC12 (PE Biosystems, Foster City, CA), 0.25 niM dNTP, 1.25 μM 5' forward and 3' reverse primer and 0.125 U of AmpliTaq DNA polymerase.

PCR mix was added to the center of cover slips (Probe-Clip Press-Seal Incubation Chamber) as spherical droplets and tissue sections were placed over the droplet. The chamber consists of a self-sealing silicone gasket along the circumference of the cover slip. Better sealing was ensured with a colorless nail polish. Alternatively, self seal reagent (MJ Research) in combination with Probe Clip cover slips was used in order to have a better sealing of the reaction materials on the whole mount embryos. Cycling reactions were done using hot start conditions by warming the slide holders to 90° C prior to placing the glass slides in the slide holders for cycling. PCR was carried out for 1 cycle at 92° C for 90 seconds followed by 30 cycles with denaturation at 94° C for 30 seconds, annealing at 50° C for 1 minutes and extension at 72° C for 1 minute. When the polymerase chain reaction was complete, samples were kept at 4° C. Cover slips were removed and the samples were heated to 92° C for 1 minute. Subsequently, slides were soaked for 5 min. in 1 x PBS at room temperature and counterstained with hematoxylin. Then samples were washed twice for 2 minutes at room temperature in 1 x PBS, post fixed in 2% paraformaldehyde and then counterstained with hematoxylin. Samples were overlaid with Permount (Fisher Scientific, Itasca, IL) and covered with cover slips.

Light Microscopy: Samples were imaged with a Zeiss two photon LSM 510 confocal microscope equipped with Ar and He/Ne lasers. Samples were excited at 633 nm/488 nm light and images collected with a 650 nm emission filter in the light path. All images were collected using standardized laser intensities and photomultiplier tube settings for amplification and dark levels. AU images were processed with Adobe

Photoshop on a Micron Millennium computer. Photomicrographs were printed out on a Kodak XLS 8500 dye sublimation printer.

While certain embodiments of the present invention have been described and/or exemplified above, it is contemplated that considerable variation and modification thereof are possible. Accordingly, the present invention is not limited to the particular embodiments described and/or exemplified herein.

All cited references are expressly incorporated herein by reference. References:

1. Reis LAG, E. M., Kosary CL, Hankey BF, Miller BA, Clegg L., Mariotto A., Fay MP, Feuer EJ, Edwards BK, SEER Cancer Statistics Review, 1975- 2000, National Cancer Institute, Bethesda, MD., 2003. 2. The 1988 Bethesda System for reporting cervical/vaginal cytological diagnoses, National Cancer Institute Workshop, Jama, 262: 931-934, 1989.

3. zur Hausen, H. Human papillomaviruses and their possible role in squamous cell carcinomas, Curr Top Microbiol Immunol, 78: 1-30, 1977.

4. Canavan, T.P. and Doshi, N.R. Cervical cancer, Am Fam Physician, 61 : 1369-1376, 2000.

5. Schiffman, M.H., Bauer, H. M., Hoover R. N., Glass A.G., Cadell, D. M., Rush, B. B., Scott, D. R., Sherman, M. E., Kurman, R. J., Wacholder, S., and et al., Epidemiologic evidence showing that human papillomavirus infection causes most cervical intraepithelial neoplasia, J. Natl. Cancer Inst., 85: 958-964, 1993. 6. Bosch, F. X., Manos, M. M., Munoz, N., Sherman, M., Jansen,

A. M., Peto, J., Schiffman, M. H., Moreno, V., Kurman, R., and Shah, K. V., Prevalence of human papillomavirus in cervical cancer: a worldwide perspective, International biological study on cervical cancer (IBSCC) Study Group, J. Natl. Cancer Inst., 87: 796-802, 1995. 7. Vainio, H., Wilbourn, J. D., Sasco, A. J., Partensky, C, Gaudin,

N., Heseltine, E., and Eragne, I. [Identification of human carcinogenic risks in IARC monographs], Bull Cancer, 82: 339-348, 1995.

8. Walboomers, J. M., Jacobs, M. V., Manos, M. M., Bosch, F. X., Kummer, J. A., Shah K. V., Snijders, P. J., Peto, J., Meijer, C. J., and Munoz, N., Human papillomavirus is a necessary cause of invasive cervical cancer worldwide., J. Pathol., 189: 12-19, 1999.

9. Schiffman, M. H. and Brinton, L. A., The epidemiology of cervical carcinogenesis., Cancer, 76: 1888-1901, 1995.

10. Brown, D. R., and Fife, K. H., Human papillomavirus infections of the genital tract, Medical Climes of North America, 74: 1455-1485, 1990.

11. Brown, D. R., Schroeder, J. M., Bryan, J. T., Staler, M. H., and Fife, K. H. , Detection of multiple human papillomavirus types in Condylomata acuminata lesions from otherwise healthy and immunosuppressed patients, Journal of Clinical Microbiology, 37: 3316-3322, 1999. 12. Brown, D. R., Legge, D., and Qadadri, B., Distribution of human papillomavirus types in cervicovaginal washings from women evaluated in a sexually transmitted diseases clinic, Sex Transm. Dis., 29: 763-768, 2002. 13. Burd, E. M., Human papillomavirus and cervical cancer, Clin. Microbiol, Rev., 16: 1-17, 2003.

14. Schiffman, M., Herrero, R., Hildesheim, A., Sherman, M. E., Bratti, M., Wacholder, S., Alfaro, M., Hutchinson, M., Morales, J., Greenberg, M.D., and Lorincz, A. T., HPV DNA testing in cervial cancer screening: results from women in a high-risk province of Costa Rica, Jama, 283: 87-93, 2000.

15. Wright, T.C., Jr., Denny, L., Kuhn, L., Pollack, A., and Lorincz, A., HPV DNA testing of self-collected vaginal samples compared with cytologic screening to detect cervical cancer., Jama, 283: 81-86, 2000. 16. Kher, R. and Bacallao, R., Direct in situ reverse transcriptase- polymerase chain reaction, Am. J. Physiol Cell Physiol., 281 : C726-732, 2001.

Claims

CLAIMS:

1. A method for identifying RNA transcripts in a patient's tissues, the method comprising the steps of: a) contacting a fixed, permeabilized tissue sample with a terra cutter restriction endonuclease; b) contacting said tissue with a DNase to produce a DNase digested tissue; c) incubating said tissue with a reverse transcriptase (RT) cocktail comprising an RT enzyme and a RT primer specific for said target nucleic acid to produce a cDNA; and d) amplifying said cDNA using a PCR reaction in the presence of forward and reverse PCR primers specific for said target nucleic acid wherein at least one of said PCR primers is labeled.

2. The method of claim 1 wherein the tissue sample is contacted with a first and second set of PCR primers wherein the first and second set of PCR primers specifically bind and amplify two different genes, and at least one of the first set of PCR primers is labeled with a first fluorophore and at least one of the second set of PCR primers is labeled with a second fluorophore, wherein the emission spectra of the first fluorophore and the second fluorophore are separately detectable when both are present.

3. The method of claim 1 wherein the RNA is a human papillomavirus mRNA transcript.

4. The method of claim 1 wherein the RNA transcript is detected directly on a slide.

5. The method of claim 1 wherein the tissue sample is a thick section of about 100 micron thick or greater.

6. The method of claim 1 wherein the tissue sample is a whole mount tissue.

7. A method for determining if a patient is at risk for or has developed cervical cancer, the method comprising the steps of, extracting a tissue or body fluid from the patient; quantifying the amount of human papillomavirus mRNA transcripts in the patient tissue or body fluid using in situ reverse transcriptase- polymerase chain reaction; and determining if the patient is at risk for or has developed cervical cancer.