# Patent

## Title
Methods and compositions for the detection of cervical disease

## Abstract

Methods and compositions for identifying high-grade cervical disease in a patient sample are provided. The methods of the invention comprise detecting overexpression of at least one biomarker in a body sample, wherein the biomarker is selectively overexpressed in high-grade cervical disease. In particular claims, the body sample is a cervical smear or monolayer of cervical cells. The biomarkers of the invention include genes and proteins that are involved in cell cycle regulation, signal transduction, and DNA replication and transcription. In particular claims, the biomarker is an S-phase gene. In some aspects of the invention, overexpression of a biomarker of interest is detected at the protein level using biomarker-specific antibodies or at the nucleic acid level using nucleic acid hybridization techniques. Kits for practicing the methods of the invention are further provided.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a divisional application of U.S. Utility application Ser. No. 11/087,227, filed Mar. 23, 2005, which claims the benefit of U.S. Provisional Application Ser. No. 60/556,495, filed Mar. 24, 2004, both of which are incorporated herein by reference in their entirety.


FIELD OF THE INVENTION
The present invention relates to methods and compositions for the detection of high-grade cervical disease.
BACKGROUND OF THE INVENTION
Carcinoma of the cervix is the second most common neoplasm in women, accounting for approximately 12% of all female cancers and causing approximately 250,000 deaths per year. Baldwin et al. (2003) Nature Reviews Cancer 3: 1-10. In many developing countries where mass screening programs are not available; the clinical problem is more serious. Cervical cancer in these countries is the number one cause of cancer deaths in women.
The majority of cases of cervical cancer represent squamous cell carcinoma, although adenocarcinoma is also seen. Cervical cancer can be prevented by population screening as it evolves through well-defined noninvasive intraepithelial stages, which can be distinguished morphologically. Williams et al. (1998) Proc. Natl. Acad. Sci. USA 95:14932-14937. While it is not understood how normal cells become transformed, the concept of a continuous spectrum of histopathological change from normal, stratified epithelium through cervical intraepithelial neoplasia (CIN) to invasive cancer has been with one or more oncogenic subtypes of HPV, there is a risk for the development of neoplasia in comparison to patients without an HPV infection. Given the importance of HPV in the development of cervical neoplasia, the clinical detection of HPV has become an important diagnostic tool in the identification of patients at risk for cervical neoplasia development. The clinical utility of HPV-based screening for cervical disease is in its negative predictive value. An HPV negative result in combination with a history of normal Pap smears is an excellent indicator of a disease-free condition and a low risk of cervical neoplasia development during the subsequent 1-3 years. However, a positive HPV result is not diagnostic of cervical disease; rather it is an indication of infection. Although the majority of HPV infections is transient and will spontaneously clear within a 12-month period, a persistent infection with a high-risk HPV viral subtype indicates a higher risk for the development of cervical neoplasia. To supplement HPV testing, the identification of molecular markers associated with cervical neoplasia is expected to improve the clinical specificity for cervical disease diagnosis.
Cytological examination of Papanicolaou-stained cervical smears (Pap smears) currently is the method of choice for detecting cervical cancer. The Pap test is a subjective method that has remained substantially unchanged for 60 years. There are several concerns, however, regarding its performance. The reported sensitivity of a single Pap test (the proportion of disease positives that are test-positive) is low and shows wide variation (30-87%). The specificity of a single Pap test (the proportion of disease negatives that are test-negative) might be as low as 86% in a screening population and considerably lower in the ASCUS PLUS population for the determination of underlying high-grade disease. See, Baldwin et al., supra. A significant percentage of Pap smears characterized as LSIL or CINI are actually positive for high-grade lesions. Furthermore, up to 10% of Pap smears are classified as ASCUS (atypical squamous cells of undetermined significance), i.e., it is not possible to make a clear categorization as normal, moderate or severe lesion, or tumor. However, experience shows that up to 10% of this ASCUS population has high-grade lesions, which are consequently overlooked. See, for example, Manos et al. (1999) JAMA 281:1605-1610.
Thus, a method for diagnosing high-grade cervical disease that is independent of or works in conjunction with conventional Pap smears and molecular testing for high-risk HPV infection is needed. Such a method should be able to specifically identify high-grade cervical disease that is present in all patient populations, including those cases classified as LSIL or CINI by Pap staining that are actually positive for high-grade lesions (i.e., “false negatives”). Therefore, there is a need in the art for specific, reliable diagnostic methods that are capable of detecting high-grade cervical disease and of differentiating high-grade disease from conditions that are not considered clinical disease, such as early-stage HPV infection and mild dysplasia.
SUMMARY OF THE INVENTION
Compositions and methods for diagnosing high-grade cervical disease are provided. The methods of the invention comprise detecting overexpression of at least one biomarker, particularly a nuclear biomarker, in a body sample, wherein the detection of overexpression of said biomarker specifically identifies samples that are indicative of high-grade cervical disease. The present method distinguishes samples that are indicative of high-grade cervical disease from samples that are indicative of benign proliferation, early-stage HPV infection, or mild dysplasia. Thus, the method relies on the detection of a biomarker that is selectively overexpressed in high-grade cervical disease states but that is not overexpressed in normal cells or cells that are not indicative of clinical disease.
The biomarkers of the invention are proteins and/or genes that are selectively overexpressed in high-grade cervical disease, including those that result from HPV-induced cell cycle dysfunction and activation of certain genes responsible for S-phase induction. Biomarkers of particular interest include S-phase genes, whose overexpression results from HPV-induced cell-cycle dysfunction and the subsequent activation of the transcriptional factors SP-1 and E2F. The detection of overexpression of the biomarker genes or proteins of the invention permits the differentiation of samples that are indicative of high-grade disease, such as moderate to severe dysplasia and cervical carcinomas, from normal cells or cells that are not indicative of clinical disease (e.g., early-stage HPV infection absent dysplasia and mild dysplasia).
Biomarker overexpression can be assessed at the protein or nucleic acid level. In some embodiments, immunocytochemistry techniques are provided that utilize antibodies to detect the overexpression of biomarker proteins in cervical cytology samples. In this aspect of the invention, at least one antibody directed to a specific biomarker of interest is used. Overexpression can also be detected by nucleic acid-based techniques, including, for example, hybridization and RT-PCR. Kits comprising reagents for practicing the methods of the invention are further provided.
The methods of the invention can also be used in combination with traditional gynecological diagnostic techniques that analyze morphological characteristics or HPV infection status. Thus, for example, the immunocytochemistry methods presented here can be combined with the Pap test so that all the morphological information from the conventional method is conserved. In this manner, the detection of biomarkers that are selectively overexpressed in high-grade cervical disease can reduce the high false-negative rate of the Pap test and may facilitate mass automated screening.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 provides a schematic summary of proliferation and cell cycle de-regulation in cervical dysplasia. Cell cycle alterations and proliferation control defects in cervical neoplasia. HPV infection and over-expression of the E6 and E7 oncoproteins produces a series of alterations in the cell cycle and proliferation control. The HPV E6 oncoprotein abrogates cell cycle checkpoints at the G1/S and G2/M boundaries with subsequent replication of DNA with somatic mutations. E7 promotes the acceleration into the S-phase with prolonged expression of the S-phase genes required for DNA replication (aberrant S-phase induction). Likewise, E6 promotes expression of telomerase ensuring continued chromosomal telomere integrity during proliferation and cellular immortalization. Finally, E7 abrogates the TGF-beta signaling pathway and abrogates this control mechanism for G1 arrest and control of proliferation.
FIG. 2 provides a schematic representation of aberrant S-phase induction in cervical neoplasia. The effects of HPV proteins on cell cycle control and proliferation include inactivation of the p53 and Rb tumor suppressor pathways, activation of E2F-1 transcription, induction of the S-phase genes MCM-2, MCM-6, MCM-7, TOP2A and Cyclin E1 along others. In addition, E2 interacts with the Sp-1 transcription factor to activate gene expression of p21-waf-1.
FIG. 3 provides a schematic representation of the feedback loop on cell proliferation in aberrant S-phase of the cell cycle. Overexpression of Cyclin E and CDK2 in the S-phase results in an independent mechanism to permit induction of the S-phase genes.
FIG. 4 provides a schematic representation of the role of c-myc in aberrant S-phase induction. C-myc is an important transcriptional activator in cellular proliferation. The gene encoding c-myc is located on the chromosome. This is the same site that HPV 18 integration has been documented with a corresponding amplification of this gene region. Amplification of the c-myc gene would result in over-expression of the encoded protein and increased levels of c-myc would independently contribute to S-phase gene transcription further accelerating cellular proliferation.
FIG. 5 provides a schematic representation of TaqMan® primers directed to MCM7 transcript variants.
FIG. 6 illustrates the differential staining pattern of an antibody directed to Claudin 1 in an IHC assay for a patient with mild dysplasia and a patient with squamous cell carcinoma.
FIG. 7 illustrates the differential staining pattern of an antibody directed to Claudin 1 in an IHC and ICC format. Normal cells and cells indicative of CINIII and HSIL are shown.
FIG. 8 illustrates nuclear staining patterns obtained with a nuclear biomarker (i.e., MCM2) and cytoplasmic staining patterns obtained with a cytoplasmic biomarker (p16). Results are from an immunocytochemistry (ICC) assay of a high-grade cervical disease patient sample.
FIG. 9 illustrates desirable and undesirable antibody staining in an immunohistochemistry (IHC) assay using two different antibodies directed to MCM6 on cervical tissue from a patient with high-grade cervical disease.



DETAILED DESCRIPTION OF THE INVENTION
The present invention provides compositions and methods for identifying or diagnosing high-grade cervical disease. The methods comprise the detection of the overexpression of specific biomarkers that are selectively overexpressed in high-grade cervical disease (e.g., moderate to severe dysplasia and cervical cancer). That is, the biomarkers of the invention are capable of distinguishing between HPV-infected cells and HPV-infected cells that are pre-malignant, malignant, or overtly cancerous. Methods for diagnosing high-grade cervical disease involve detecting the overexpression of at least one biomarker that is indicative of high-grade cervical disease in a tissue or body fluid sample from a patient. In particular embodiments, antibodies and immunocytochemistry techniques are used to detect expression of the biomarker of interest. Kits for practicing the methods of the invention are further provided.
“Diagnosing high-grade cervical disease” is intended to include, for example, diagnosing or detecting the presence of cervical disease, monitoring the progression of the disease, and identifying or detecting cells or samples that are indicative of high-grade cervical disease. The terms diagnosing, detecting, and identifying high-grade cervical disease are used interchangeably herein. By “high-grade cervical disease” is intended those conditions classified by colposcopy as premalignant pathology, malignant pathology, moderate to severe dysplasia, and cervical cancer. Underlying high-grade cervical disease includes histological identification of CINII, CINIII, HSIL, carcinoma in situ, adenocarcinoma, and cancer (FIGO stages I-IV).
As discussed above, a significant percentage of patients presenting with Pap smears classified as normal, CINI, or ASCUS actually have lesions characteristic of high-grade cervical disease. Thus, the methods of the present invention permit the identification of high-grade cervical disease in all patient populations, including these “false negative” patients, and facilitate the detection of rare abnormal cells in a patient sample. The diagnosis can be made independent of cell morphology and HPV infection status, although the methods of the invention can also be used in conjunction with conventional diagnostic techniques, e.g., Pap test, molecular testing for high-risk types of HPV, etc.
HPV types have been divided into high and low-risk categories based on their association with cervical cancer and precancerous lesions. Low-risk HPV types include types 6, 11, 42, 43, 44 and are not associated with an increased risk of cervical cancer. In contrast, high-risk HPV types, including types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68, have been strongly associated with cervical cancer and squamous intraepithelial lesions. See, for example, Wright et al. (2004) Obstet. Gynecol. 103:304-309. In fact, over 99% of cervical cancers are associated with high-risk HPV infection. Persistent high-risk HPV infection leads to the disruption of the cell cycle and mitotic checkpoints in cervical cells through the action of HPV genes E2, E6, and E7. In particular, HPV E7 causes an increase in cyclin E and the subsequent release of the transcription factor E2f from the retinoblastoma (Rb) protein. The released E2f transcription factor then triggers the transcription of a variety of S-phase genes, including topoisomerase II alpha (Topo2A), MCM proteins, cyclins E1 and E2, and p14arf, resulting in loss of cell cycle control. HPV E2 further stimulates overexpression of S-phase genes such as p21waf-1 by activating the Sp-1 transcription factor. The cell cycle disruption caused by persistent HPV infection can lead to mild cervical dysplasia that may then progress to moderate or severe dysplasia and eventually to cervical cancer in some cases. By “cervical cancer” is intended any cancer or cancerous lesion associated with cervical tissue or cervical cells.
HPV infection within cervical keratinocytes results in a number of alterations that disrupt the activities within the cell cycle. The E6 and E7 oncoproteins of the high-risk HPV subtypes have been implicated in a number of cellular processes related to increased proliferation and neoplastic transformation of the infected keratinocytes. The E6 protein has been implicated in two critical processes. The first is the degradation of the p53 tumor suppressor protein through ubiquitin-mediated proteolysis. Removal of functional p53 eliminates a major cell cycle checkpoint responsible for DNA repair prior to entry into DNA replication and mitosis (Duensing and Munger (2003) Prog Cell Cycle Res. 5:383-391). In addition, E6 has been shown to interact with the c-myc protein and is responsible for direct transcriptional activation of the hTERT gene with subsequent expression of telomerase (McMurray and McCance (2003) J Virol. 77:9852-9861; Veldman et al. (2003) Proc Natl Acad Sci U.S.A. 100: 8211-8216). Activation of telomerase is a key step in cancer biology responsible for the maintenance of telomere length on replicating chromosomes and this enzyme ensures functionally intact chromosomes during cellular immortalization.
The HPV oncoprotein E7 is known to contribute to cellular proliferation through two independent mechanisms. The first is the inactivation of the TGF-beta tumor suppressor pathway responsible for cell cycle arrest at the G1 phase through direct interaction of E7 with the Smad proteins (Smad 2, 3 and 4), thereby inhibiting their ability to bind to DNA (Lee et al. (2002) J Biol Chem. 277:38557-38564). Likewise, E7 is known to specifically interact with the Rb tumor suppressor protein. Within the G1 phase of the cell cycle, Rb complexes the E2F transcription factor and prevents E2F from activating gene transcription. At the G1/S boundary, the Rb protein is phosphorylated with release of the E2F transcription factor—thereby initiating E2F gene transcription and entry into the S phase of the cell cycle. The HPV E7 oncoprotein abrogates this control mechanism by directly binding with Rb and displacing E2F from the complex. This results in E2F driven gene transcription independent of normal cell cycle control (Duensing and Munger (2003) Prog Cell Cycle Res. 5:383-391; Duensing and Munger (2004) Int J Cancer 109:157-162; Clarke and Chetty (2001) Gynecol Oncol. 82:238-246). This release of E2F uncouples gene transcription from cell cycle control and results in prolonged and aberrant transcription of S-phase genes responsible for DNA synthesis and cellular proliferation. In addition, the combined actions of both E6 and E7 have been shown to contribute to centrosome abnormalities and the subsequent genomic instability in cervical neoplasia (Duensing and Munger (2004) Int J Cancer 109:157-162).
While not intending to be limited to a particular mechanism, in some embodiments, the molecular behavior of high-grade cervical disease can be characterized as the overexpression of discrete genes, normally expressed only during the S-phase of the cell cycle, as a result of infection by oncogenic strains of HPV. The subsequent uncontrolled activation of gene transcription and aberrant S-phase induction is mediated through the E2F-1 transcription factor pathway. This behavior appears to be indicative of high-grade cervical disease and provides a link between oncogenic HPV infections and the molecular behavior of cervical neoplasia. The use of these molecular biomarkers of cervical neoplasia in molecular diagnostic assay formats can improve the detection of cervical disease with an improved sensitivity and specificity over current methods. See generally FIGS. 1-4 and Malinowski (2005) BioTechniques 38:1-8 (in press), which is herein incorporated by reference in its entirety. Thus, in particular embodiments, a method for diagnosing high-grade cervical disease comprises detecting overexpression of a biomarker, wherein overexpression of the biomarker is indicative of aberrant S-phase induction, as described herein. In still other embodiments, the methods comprise detecting overexpression of a biomarker, wherein overexpression of the biomarker is indicative of active transcription or overexpression of the HPV E6 and HPV E7 genes.
Dysplasia is conventionally defined in morphological terms by a loss of normal orientation of epithelial cells, accompanied by alterations in cellular and nuclear size, shape, and staining characteristics. Dysplasia is graded according to the degree of the cellular abnormalities (i.e., mild, moderate, severe) and is widely accepted to be an intermediate stage in the progression from normal tissue to neoplasia, as evidenced by the identification of pre-malignant dysplastic conditions such as CIN. The methods of the present invention permit the identification of high-grade cervical disease, which includes moderate to severe dysplasia and cervical cancer (i.e., CINII conditions and above), based on the overexpression of biomarkers that are specific to high-grade cervical disease.
The methods disclosed herein provide superior detection of high-grade cervical disease in comparison to PAP smears and/or HPV infection testing. In particular aspects of the invention, the sensitivity and specificity of the present methods are equal to or greater than that of conventional Pap smears. As used herein, “specificity” refers to the level at which a method of the invention can accurately identify samples that have been confirmed as NIL by colposcopy (i.e., true negatives). That is, specificity is the proportion of disease negatives that are test-negative. In a clinical study, specificity is calculated by dividing the number of true negatives by the sum of true negatives and false positives. By “sensitivity” is intended the level at which a method of the invention can accurately identify samples that have been colposcopy-confirmed as positive for high-grade cervical disease (i.e., true positives). Thus, sensitivity is the proportion of disease positives that are test-positive. Sensitivity is calculated in a clinical study by dividing the number of true positives by the sum of true positives and false negatives. See Examples 1-3 below. In some embodiments, the sensitivity of the disclosed methods for the detection of high-grade cervical disease is preferably at least about 70%, more preferably at least about 80%, most preferably at least about 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% or more. Furthermore, the specificity of the present methods is preferably at least about 70%, more preferably at least about 80%, most preferably at least about 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% or more.
The term “positive predictive value” or “PPV” refers to the probability that a patient has high-grade cervical disease when restricted to those patients who are classified as positive using a method of the invention. PPV is calculated in a clinical study by dividing the number of true positives by the sum of true positives and false positives. In some embodiments, the PPV of a method of the invention for diagnosing high-grade cervical disease is at least about 40%, while maintaining a sensitivity of at least about 90%, more particularly at least about 95%. The “negative predictive value” or “NPV” of a test is the probability that the patient will not have the disease when restricted to all patients who test negative. NPV is calculated in a clinical study by dividing the number of true negatives by the sum of true negatives and false negatives.
The biomarkers of the invention include genes and proteins, and variants and fragments thereof. Such biomarkers include DNA comprising the entire or partial sequence of the nucleic acid sequence encoding the biomarker, or the complement of such a sequence. The biomarker nucleic acids also include RNA comprising the entire or partial sequence of any of the nucleic acid sequences of interest. A biomarker protein is a protein encoded by or corresponding to a DNA biomarker of the invention. A biomarker protein comprises the entire or partial amino acid sequence of any of the biomarker proteins or polypeptides.
A “biomarker” is any gene or protein whose level of expression in a tissue or cell is altered compared to that of a normal or healthy cell or tissue. Biomarkers of the invention are selective for underlying high-grade cervical disease. By “selectively overexpressed in high-grade cervical disease” is intended that the biomarker of interest is overexpressed in high-grade cervical disease but is not overexpressed in conditions classified as LSIL, CINI, HPV-infected samples without any dysplasia present, immature metaplastic cells, and other conditions that are not considered to be clinical disease. Thus, detection of the biomarkers of the invention permits the differentiation of samples indicative of underlying high-grade cervical disease from samples that are indicative of benign proliferation, early-stage HPV infection, or mild dysplasia. By “early-stage HPV infection” is intended HPV infection that has not progressed to cervical dysplasia. As used herein, “mild dysplasia” refers to LSIL and CINI where no high-grade lesion is present. The methods of the invention also distinguish cells indicative of high-grade disease from normal cells, immature metaplastic cells, and other cells that are not indicative of clinical disease. In this manner, the methods of the invention permit the accurate identification of high-grade cervical disease, even in cases mistakenly classified as normal, CINI, LSIL, or ASCUS by traditional Pap testing (i.e., “false negatives”). In some embodiments, the methods for diagnosing high-grade cervical disease are performed as a reflex to an abnormal or atypical Pap smear. That is, the methods of the invention may be performed in response to a patient having an abnormal or atypical Pap smear result. In other aspects of the invention, the methods are performed as a primary screening test for high-grade cervical disease in the general population of women, just as the conventional Pap test is performed currently.
The biomarkers of the invention include any gene or protein that is selectively overexpressed in high-grade cervical disease, as defined herein above. Such biomarkers are capable of identifying cells within a cytology cell suspension that are pre-malignant, malignant, or overtly cancerous. The biomarkers of the invention detect cells of CINII conditions and above, but do not detect CINI and HPV-infected cells where there is no underlying high-grade disease. Biomarkers of particular interest include genes and proteins involved in cell cycle regulation, HPV disruption of the cell cycle, DNA replication and transcription, and signal transduction. In some embodiments, the biomarkers are S-phase genes, including those genes whose expression is stimulated by the E2f transcription factor or the Sp-1 transcription factor. Nuclear biomarkers may be used to practice certain aspects of the invention. By “nuclear biomarker” is intended a biomarker that is predominantly expressed in the nucleus of the cell. A nuclear widely accepted for years. The precursor to cervical cancer is dysplasia, also known in the art as CIN or squamous intraepithelial lesions (SIL). Squamous intraepithelial abnormalities may be classified by using the three-tiered (CIN) or two-tiered (Bethesda) system. Under the Bethesda system, low-grade squamous intraepithelial lesions (LSIL), corresponding to CINI and HPV infection, generally represent productive HPV infections with a relatively low risk of progression to invasive disease. High-grade squamous intraepithelial lesions (HSIL), corresponding to CINII and CINIII in the three-tiered system, show a higher risk of progression to cervical cancer than do LSIL, although both LSIL and HSIL are viewed as potential precursors of malignancy. Patient samples may also be classified as ASCUS (atypical squamous cells of unknown significance) or AGUS (atypical glandular cells of unknown significance) under this system.
A strong association of cervical cancer and infection by high-risk types of human papilloma virus (HPV), such as types 16, 18, and 31, has been established. In fact, a large body of epidemiological and molecular biological evidence has established HPV infection as a causative factor in cervical cancer. Moreover, HPV is found in 85% or more of the cases of high-grade cervical disease. However, HPV infection is very common, possibly occurring in 5-15% of women over the age of 30, but few HPV-positive women will ever develop high-grade cervical disease or cancer. The presence of HPV alone is indicative only of infection, not of high-grade cervical disease, and, therefore, testing for HPV infection alone results in many false positives. See, for example, Wright et al. (2004) Obstet. Gynecol. 103:304-309.
Current literature suggests that HPV infects the basal stem cells within the underlying tissue of the uterine-cervix. Differentiation of the stem cells into mature keratinocytes, with resulting migration of the cells to the stratified cervical epithelium, is associated with HPV viral replication and re-infection of cells. During this viral replication process, a number of cellular changes occur that include cell-cycle de-regulation, active proliferation, DNA replication, transcriptional activation and genomic instability (Crum (2000) Modern Pathology 13:243-251; Middleton et al (2003) J. Virol. 77:10186-10201; Pett et al. (2004) Cancer Res. 64:1359-1368).
Most HPV infections are transient in nature, with the viral infection resolving itself within a 12-month period. For those individuals who develop persistent infections biomarker may be expressed to a lesser degree in other parts of the cell. Although any biomarker indicative of high-grade cervical disease may be used in the present invention, in certain embodiments the biomarkers, particularly nuclear biomarkers, are selected from the group consisting of MCM2, MCM6, MCM7, p21waf1, topoisomerase II alpha (Topo2A), p14arf, and cyclin E. More particularly, the biomarker may comprise an MCM protein.
Minichromosome maintenance (MCM) proteins play an essential part in eukaryotic DNA replication. The minichromosome maintenance (MCM) proteins function in the early stages of DNA replication through loading of the prereplication complex onto DNA and functioning as a helicase to help unwind the duplex DNA during de novo synthesis of the duplicate DNA strand. Each of the MCM proteins has DNA-dependent ATPase motifs in their highly conserved central domain. Levels of MCM proteins generally increase in a variable manner as normal cells progress from G0 into the G1/S phase of the cell cycle. In the G0 phase, MCM2 and MCM5 proteins are much less abundant than are the MCM7 and MCM3 proteins. MCM6 forms a complex with MCM2, MCM4, and MCM7, which binds histone H3. In addition, the subcomplex of MCM4, MCM6, and MCM7 has helicase activity, which is mediated by the ATP-binding activity of MCM6 and the DNA-binding activity of MCM4. See, for example, Freeman et al. (1999) Clin. Cancer Res. 5:2121-2132; Lei et al. (2001) J. Cell Sci. 114:1447-1454; Ishimi et al. (2003) Eur. J. Biochem. 270:1089-1101, all of which are herein incorporated by reference in their entirety.
Early publications have shown that the MCM proteins, and in particular, MCM-5, are useful for the detection of cervical disease (Williams et al. (1998) Proc Natl Acad Sci U.S.A. 95:14932-14937), as well as other cancers (Freeman et al. (1999) Clin Cancer Res. 5:2121-2132). The published literature indicates that antibodies to MCM-5 are capable of detecting cervical neoplastic cells. The specificity for detection of high-grade cervical disease has not been demonstrated for MCM-5 (Williams et al. (1998) Proc Natl Acad Sci U.S.A. 95:14932-14937). The detection of MCM-5 expression is not restricted to high-grade cervical disease but is also detected in identified low-grade dysplasia and proliferative cells that have re-entered the cell cycle following infection with high-risk HPV. The detection of cervical neoplasia with antibodies to MCM-5 is shown in FIG. 4. In addition to MCM-5, other members from the MCM family, including MCM-2 and MCM-7 have been shown to be potentially useful markers for the detection of cervical neoplasia in tissue samples (Freeman et al. (1999) Clin Cancer Res. 5:2121-2132; Brake et al. (2003) Cancer Res. 63:8173-8180). Recent results have shown that MCM-7 appears to be a specific marker for the detection of high-grade cervical disease using immunochemistry formats (Brake et al. (2003) Cancer Res. 63:8173-8180; Malinowski et al. (2004) Acta Cytol. 43:696).
Topoisomerase II alpha (Topo2a) is an essential nuclear enzyme involved in DNA replication and is a target for many anti-cancer drugs used for cancer therapy. Decreased expression of Topo2a is a predominant mechanism of resistance to several chemotherapeutic agents. A significant variation in the range of expression of this protein has been noted in many different tumors. Topo2a is predominant in proliferating cells and is modified in M phase by phosphorylation at specific sites, which is critical for mitotic chromosome condensation and segregation.
p21 is a protein encoded by the WAF1/Cip1 gene on chromosome 6p. This gene was shown to inhibit the activity of several cyclin/cyclin-dependent kinase complexes and to block cell cycle progression. The expression of p21waf1 mediates the cell cycle arrest function of p53. Because p21 appears to mediate several of the growth-regulatory functions of p53, its expression may reflect the functional status of p53 more precisely than p53 accumulation. Furthermore, p21waf1 can inhibit DNA replication by blocking the action of proliferating cell nuclear antigen (PCNA).
Cyclin E is a regulatory subunit of cdk-2 and controls G1/S transition during the mammalian cell cycle. Multiple isoforms of Cyclin E are expressed only in tumors but not in the normal tissues, suggesting a post-transcriptional regulation of Cyclin E. In vitro analyses indicated that these truncated variant isoforms of Cyclin E are able to phosphorylate histone H1. Alterations in Cyclin E proteins have been implicated as indicators of poor prognosis in various cancers.
Although the above biomarkers have been discussed in detail, any biomarker that is overexpressed in high-grade cervical disease states (e.g., CINII, CINIII, and cervical carcinomas) may be used in the practice of the invention. Other biomarkers of interest include cell cycle regulated genes that are specific to the G1/S phase boundary or to S-phase. Such genes include but are not limited to helicase (DD×11), uracil DNA glycolase (UNG), E2F5, cyclin E1 (CCNE1), cyclin E2 (CCNE2), CDC25A, CDC45L, CDC6, p21 WAF-1(CDKN1A), CDKN3, E2F1, MCM2, MCM6, NPAT, PCNA, stem loop BP (SLBP), BRCA1, BRCA2, CCNG2, CDKN2C, dihydrofolate reductase (DHFR), histone H1, histone H2A, histone H2B, histone H3, histone H4, MSH2, NASP, ribonucleotide reductase M1 (RRM1), ribonucleotide reductase M2 (RRM2), thymidine synthetase (TYMS), replication factor C4 (RFC4), RAD51, chromatin Factor 1A (CHAF1A), chromatin Factor 1B (CHAF1B), topisomerase III (TOP3A), ORC1, primase 2A (PRIM2A), CDC27, primase 1 (PRIM1), flap structure endonuclease (FEN1), fanconi anemia comp. grp A (FNACA), PKMYT1, and replication protein A2 (RPA2). See, for example, Whitfield et al. (2002) Mol. Biol. Cell 13:1977-2000, herein incorporated by reference in its entirety. Other S phase genes of interest include cyclin-dependent kinase 2 (CDK2), MCM3, MCM4, MCM5, DNA polymerase I alpha (DNA POL1), DNA ligase 1, B-Myb, DNA methyl transferase (DNA MET), pericentrin (PER), KIF4, DP-1, ID-3, RAN binding protein (RANBP1), gap junction alpha 6 (GJA6), amino levulinate dehydratase (ALDH), histone 2A Z (H2A.Z), spermine synthase (SpmS), proliferin 2, T-lymphocyte activation protein, phospholipase A2 (PLA2), and L6 antigen (L6). See, for example, Nevins et al. (2001) Mol. Cell. Biol. 21:4689-4699, herein incorporated by reference.
In some aspects of the invention, the biomarkers comprise genes that are induced by the E2f transcription factor. Such genes include but are not limited to thymidylate synthase, thymidine kinase 1, ribonucleotide reductase M1, ribonucleotide reductase M2, CDK2, cyclin E, MCM3, MCM7, PCNA, DNA primase small subunit, topoisomerase II A (Topo2A), DNA ligase 1, flap endonuclease 1, RAD51, CDC2, cyclin A2, cyclin B1, cyclin B2, KI-67, KIFC1, FIN16, BUB1, importin alpha-2, HMG2, enhancer of zeste, STK-1, histone stem-loop BP, Rb, P18-INK4C, annexin VIII, c-Myb, CDC25A, cyclin D3, cyclin E1, deoxycytosine kinase, DP-1, endothelin converting enzyme, enolase 2, P18 INK4C, ribonucleotide reductase, and uracil DNA glycolase 2. See, for example Nevins et al., supra; Muller et al. (2000) Genes and Dev. 15:267-285. In particular embodiments the biomarker of interest is a gene induced by E2f transcription factor that is involved in cell cycle regulation and DNA replication, such as, for example, cyclin E2, Ki-67, p57KIP2, RANBPM, and replication protein A1. Some E2f-induced genes of interest are involved in apoptosis, including APAF1, Bcl-2, caspase 3, MAP3 Kinase 5, and TNF receptor associated factor. Other E2f-induced genes are involved in the regulation of transcription and include, for example, ash2 like, polyhomeotic 2, embryonic ectoderm protein, enhancer of zeste, hairy/enhancer of split, homeobox A110, homeobox A7, homeobox A9, homeodomain TF1, pre-B-cell leukemia FT3, YY1 TF, POU domain TF, TAFII130, TBP-factor 172, basic TF3, bromodomain/zinc finger, SWI/SNF, ID4, TEA-4, NFATC1, NFATC3, BT, CNC-1, MAF, MAFF, MAFG, core binding protein, E74-like factor 4, c-FOS, JUNB, zinc finger DNA BP, and Cbp/p300 transactivator. E2f-induced genes involved in signal transduction are also potential biomarkers of interest and include TGF beta, follistatin, bone morphogenetic protein 2, BMP receptor type 1A, frizzled homolog 1, WNT10B, sphingosine kinase 1, dual specificity phosphatase 7, dual specificity (Y) phosphatase, FGF Receptor 3, protein tyrosine phosphatase, dual specificity (Y) phosphatase D6655, insulin receptor, mature T-cell proliferation 1, FGF receptor 2, TGF alpha, CDC42 effector protein 3, Met, CD58, CD83, TACC1, and TEAD4.
Although the methods of the invention require the detection of at least one biomarker in a patient sample for the detection of high-grade cervical disease, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more biomarkers may be used to practice the present invention. It is recognized that detection of more than one biomarker in a body sample may be used to identify instances of high-grade cervical disease. Therefore, in some embodiments, two or more biomarkers are used, more preferably, two or more complementary biomarkers. By “complementary” is intended that detection of the combination of biomarkers in a body sample results in the successful identification of high-grade cervical disease in a greater percentage of cases than would be identified if only one of the biomarkers was used. Thus, in some cases, a more accurate determination of high-grade cervical disease can be made by using at least two biomarkers. Accordingly, where at least two biomarkers are used, at least two antibodies directed to distinct biomarker proteins will be used to practice the immunocytochemistry methods disclosed herein. The antibodies may be contacted with the body sample simultaneously or concurrently. In certain aspects of the invention, the overexpression of MCM2 and Topo2A is detected using three antibodies, wherein two of the antibodies are specific for MCM2 and the third antibody is specific for Topo2A.
In particular embodiments, the diagnostic methods of the invention comprise collecting a cervical sample from a patient, contacting the sample with at least one antibody specific for a biomarker of interest, and detecting antibody binding. Samples that exhibit overexpression of a biomarker of the invention, as determined by detection of antibody binding, are deemed positive for high-grade cervical disease. In particular embodiments, the body sample is a monolayer of cervical cells. In some aspects of the invention, the monolayer of cervical cells is provided on a glass slide.
By “body sample” is intended any sampling of cells, tissues, or bodily fluids in which expression of a biomarker can be detected. Examples of such body samples include but are not limited to blood, lymph, urine, gynecological fluids, biopsies, and smears. Body samples may be obtained from a patient by a variety of techniques including, for example, by scraping or swabbing an area or by using a needle to aspirate bodily fluids. Methods for collecting various body samples are well known in the art. In particular embodiments, the body sample comprises cervical cells, as cervical tissue samples or as cervical cells in suspension, particularly in a liquid-based preparation. In one embodiment, cervical samples are collected according to liquid-based cytology specimen preparation guidelines such as, for example, the SurePath® (TriPath Imaging, Inc.) or the ThinPrep® preparation (CYTYC, Inc.). Body samples may be transferred to a glass slide for viewing under magnification. Fixative and staining solutions may be applied to the cells on the glass slide for preserving the specimen and for facilitating examination. In one embodiment the cervical sample will be collected and processed to provide a monolayer sample, as set forth in U.S. Pat. No. 5,346,831, herein incorporated by reference.
The monolayer method relates to a method for producing a monolayer of cytological material on a cationically-charged substrate. The method comprises the steps of separating the cytological material by centrifugation over a density gradient, producing a packed pellet of the cytological material, mixing the pellet of the cytological material, withdrawing an aliquot of a predetermined volume from the mixed pellet, depositing the aliquot and a predetermined volume of water into a sedimentation vessel, which is removably secured to the cationically-charged substrate, allowing the cytological material to settle onto the substrate under the force of gravity, and after settlement of the cytological material, removing the water from the sedimentation vessel. For automated analysis, the sedimentation vessel may be detached from the substrate. Disaggregation may be by any methods known in the art, such as syringing, trypsinizing, ultrasonication, shaking, vortexing, or by use of the device described in copending U.S. Pat. No. 5,316,814, the contents of which are herein incorporated by reference. In some embodiments, slides comprising a monolayer of cervical cells are prepared from SurePathTM (TriPath Imaging, Inc.) samples using the PrepStainTM slide processor (TriPath Imaging, Inc.).
Any methods available in the art for identification or detection of the biomarkers are encompassed herein. The overexpression of a biomarker of the invention can be detected on a nucleic acid level or a protein level. In order to determine overexpression, the body sample to be examined may be compared with a corresponding body sample that originates from a healthy person. That is, the “normal” level of expression is the level of expression of the biomarker in cervical cells of a human subject or patient not afflicted with high-grade cervical disease. Such a sample can be present in standardized form. In some embodiments, particularly when the body sample comprises a monolayer of cervical cells, determination of biomarker overexpression requires no comparison between the body sample and a corresponding body sample that originates from a healthy person. In this situation, the monolayer of cervical cells from a single patient may contain as few as 1-2 abnormal cells per 50,000 normal cells present. Detection of these abnormal cells, identified by their overexpression of a biomarker of the invention, precludes the need for comparison to a corresponding body sample that originates from a healthy person.
Methods for detecting biomarkers of the invention comprise any methods that determine the quantity or the presence of the biomarkers either at the nucleic acid or protein level. Such methods are well known in the art and include but are not limited to western blots, northern blots, southern blots, ELISA, immunoprecipitation, immunofluorescence, flow cytometry, immunocytochemistry, nucleic acid hybridization techniques, nucleic acid reverse transcription methods, and nucleic acid amplification methods. In particular embodiments, overexpression of a biomarker is detected on a protein level using, for example, antibodies that are directed against specific biomarker proteins. These antibodies can be used in various methods such as Western blot, ELISA, immunoprecipitation, or immunocytochemistry techniques. Likewise, immunostaining of cervical smears can be combined with conventional Pap stain methods so that morphological information and immunocytochemical information can be obtained. In this manner, the detection of the biomarkers can reduce the high false-negative rate of the Pap smear test and may facilitate mass automated screening.
In one embodiment, antibodies specific for biomarker proteins are utilized to detect the overexpression of a biomarker protein in a body sample. The method comprises obtaining a body sample from a patient, contacting the body sample with at least one antibody directed to a biomarker that is selectively overexpressed in high-grade cervical disease, and detecting antibody binding to determine if the biomarker is overexpressed in the patient sample. A preferred aspect of the present invention provides an immunocytochemistry technique for diagnosing high-grade cervical disease. Specifically, this method comprises antibody staining of biomarkers within a patient sample that are specific for high-grade cervical disease. One of skill in the art will recognize that the immunocytochemistry method described herein below may be performed manually or in an automated fashion using, for example, the Autostainer Universal Staining System (Dako) or the Biocare Nemesis Autostainer (Biocare). One protocol for antibody staining (i.e., immunocytochemistry) of cervical samples is provided in Example 1.
In a preferred immunocytochemistry method, a patient cervical sample is collected into a liquid medium, such as, for example, in a SurePathTM collection vial (TriPath Imaging, Inc.). An automated processor such as the PrepStainTM system (TriPath Imaging, Inc.) is used to collect cells from the liquid medium and to deposit them in a thin layer on a glass slide for further analysis. Slide specimens may be fixed or unfixed and may be analyzed immediately following preparation or may be stored for later analysis. In some embodiments, prepared slides are stored in 95% ethanol for a minimum of 24 hours. Alternatively, in other embodiments, slides are stored in a pretreatment buffer, as described below.
Samples may need to be modified in order to make the biomarker antigens accessible to antibody binding. In a particular aspect of the immunocytochemistry methods, slides are transferred to a pretreatment buffer, for example the SureSlide® Preparation Buffer (TriPath Imaging, Inc.) and optionally heated to increase antigen accessibility. Heating of the sample in the pretreatment buffer rapidly disrupts the lipid bi-layer of the cells and makes the antigens (i.e., biomarker proteins) more accessible for antibody binding. The pretreatment buffer may comprise a polymer, a detergent, or a nonionic or anionic surfactant such as, for example, an ethyloxylated anionic or nonionic surfactant, an alkanoate or an alkoxylate or even blends of these surfactants or even the use of a bile salt. In particular embodiments, the pretreatment buffer comprises a nonionic or anionic detergent, such as sodium alkanoate with an approximate molecular weight of 183 kD blended with an alkoxylate with an approximate molecular weight of 370 kD (hereafter referred to as RAM). In a particular embodiment, the pretreatment buffer comprises 1% RAM. In some embodiments, the pretreatment buffer may also be used as a slide storage buffer, as indicated above. In another embodiment a solution of 0.1% to 1% of deoxycholic acid, sodium salt, monohydrate was used as both a storage buffer as well as a pretreatment buffer. In yet another embodiment of the invention a solution of sodium laureth-13-carboxylate (e.g., Sandopan LS) or and ethoxylated anionic complex or even an alkylaryl ethoxlate carboxylic acid can be used for the storage and pretreatment buffers. In a particular aspect of the invention, the slide pretreatment buffer comprises 0.05% to 5% sodium laureth-13-carboxylate, particularly 0.1% to 1% sodium laureth-13-carboxylate, more particularly 0.5% sodium laureth-13-carboxylate. In one embodiment the slides can be stored in the buffer for up to 72 hours prior to the pretreatment and staining process. The pretreatment buffers of the invention may be used in methods for making antigens more accessible for antibody binding in an immunoassay, such as, for example, an immunocytochemistry method or an immunohistochemistry method. See Example 14. The terms “pretreatment buffer” and “preparation buffer” are used interchangeably herein to refer to a buffer that is used to prepare cytology or histology samples for immunostaining, particularly by increasing antigen accessibility for antibody binding.
Any method for making antigens more accessible for antibody binding may be used in the practice of the invention, including the antigen retrieval methods known in the art. See, for example, Bibbo et al. (2002) Acta. Cytol. 46:25-29; Saqi et al. (2003) Diagn. Cytopathol. 27:365-370; Bibbo et al. (2003) Anal. Quant. Cytol. Histol. 25:8-11, herein incorporated by reference in their entirety. In some embodiments, antigen retrieval comprises storing the slides in 95% ethanol for at least 24 hours, immersing the slides in 1× Target Retrieval Solution pH 6.0 (DAKO S1699)/dH2O bath preheated to 95° C., and placing the slides in a steamer for 25 minutes. See Example 2 below.
Following pretreatment or antigen retrieval to increase antigen accessibility, samples are blocked using an appropriate blocking agent, e.g., a peroxidase blocking reagent such as hydrogen peroxide. In some embodiments, the samples are blocked using a protein blocking reagent to prevent non-specific binding of the antibody. The protein blocking reagent may comprise, for example, purified casein. An antibody, particularly a monoclonal antibody, directed to a biomarker of interest is then incubated with the sample. As noted above, one of skill in the art will appreciate that a more accurate diagnosis of high-grade cervical disease may be obtained in some cases by detecting more than one biomarker in a patient sample. Therefore, in particular embodiments, at least two antibodies directed to two distinct biomarkers are used to detect high-grade cervical disease. Where more than one antibody is used, these antibodies may be added to a single sample sequentially as individual antibody reagents or simultaneously as an antibody cocktail. See Example 3 below. Alternatively, each individual antibody may be added to a separate sample from the same patient, and the resulting data pooled. In particular embodiments, an antibody cocktail comprises at least three antibodies, wherein two antibodies specifically bind to MCM2 and a third antibody specifically binds to Topo2A.
Techniques for detecting antibody binding are well known in the art. Antibody binding to a biomarker of interest may be detected through the use of chemical reagents that generate a detectable signal that corresponds to the level of antibody binding and, accordingly, to the level of biomarker protein expression. In one of the immunocytochemistry methods of the invention, antibody binding is detected through the use of a secondary antibody that is conjugated to a labeled polymer. Examples of labeled polymers include but are not limited to polymer-enzyme conjugates. The enzymes in these complexes are typically used to catalyze the deposition of a chromogen at the antigen-antibody binding site, thereby resulting in cell staining that corresponds to expression level of the biomarker of interest. Enzymes of particular interest include horseradish peroxidase (HRP) and alkaline phosphatase (AP). Commercial antibody detection systems, such as, for example the Dako Envision+ system and Biocare Medical's Mach 3 system, may be used to practice the present invention.
In one particular immunocytochemistry method of the invention, antibody binding to a biomarker is detected through the use of an HRP-labeled polymer that is conjugated to a secondary antibody. Antibody binding can also be detected through the use of a mouse probe reagent, which binds to mouse monoclonal antibodies, and a polymer conjugated to HRP, which binds to the mouse probe reagent. Slides are stained for antibody binding using the chromogen 3,3-diaminobenzidine (DAB) and then counterstained with hematoxylin and, optionally, a bluing agent such as ammonium hydroxide or TBS/Tween-20. In some aspects of the invention, slides are reviewed microscopically by a cytotechnologist and/or a pathologist to assess cell staining (i.e., biomarker overexpression) and to determine if high-grade cervical disease is present. Alternatively, samples may be reviewed via automated microscopy or by personnel with the assistance of computer software that facilitates the identification of positive staining cells.
The terms “antibody” and “antibodies” broadly encompass naturally occurring forms of antibodies and recombinant antibodies such as single-chain antibodies, chimeric and humanized antibodies and multi-specific antibodies as well as fragments and derivatives of all of the foregoing, which fragments and derivatives have at least an antigenic binding site. Antibody derivatives may comprise a protein or chemical moiety conjugated to the antibody.
“Antibodies” and “immunoglobulins” (Igs) are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to an antigen, immunoglobulins include both antibodies and other antibody-like molecules that lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas.
The term “antibody” is used in the broadest sense and covers fully assembled antibodies, antibody fragments that can bind antigen (e.g., Fab′, F′(ab)2, Fv, single chain antibodies, diabodies), and recombinant peptides comprising the foregoing.
The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally-occurring mutations that may be present in minor amounts.
“Antibody fragments” comprise a portion of an intact antibody, preferably the antigen-binding or variable region of the intact antibody. Examples of antibody fragments include Fab, Fab′, F(ab′)2, and Fv fragments; diabodies; linear antibodies (Zapata et al. (1995) Protein Eng. 8(10):1057-1062); single-chain antibody molecules; and multispecific antibodies formed from antibody fragments. Papain digestion of antibodies produces two identical antigen-binding fragments, called “Fab” fragments, each with a single antigen-binding site, and a residual “Fc” fragment, whose name reflects its ability to crystallize 35 readily. Pepsin treatment yields an F(ab′)2 fragment that has two antigen-combining sites and is still capable of cross-linking antigen.
“Fv” is the minimum antibody fragment that contains a complete antigen recognition and binding site. In a two-chain Fv species, this region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association. In a single-chain Fv species, one heavy- and one light-chain variable domain can be covalently linked by flexible peptide linker such that the light and heavy chains can associate in a “dimeric” structure analogous to that in a two-chain Fv species. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the VH-VL dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.
The Fab fragment also contains the constant domain of the light chain and the first constant domain (CH1) of the heavy chain. Fab fragments differ from Fab′ fragments by the addition of a few residues at the carboxy terminus of the heavy-chain CH1 domain including one or more cysteines from the antibody hinge region. Fab′-SH is the designation herein for Fab′ in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab′)2 antibody fragments originally were produced as pairs of Fab′ fragments that have hinge cysteines between them.
Polyclonal antibodies can be prepared by immunizing a suitable subject (e.g., rabbit, goat, mouse, or other mammal) with a biomarker protein immunogen. The antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized biomarker protein. At an appropriate time after immunization, e.g., when the antibody titers are highest, antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein (1975) Nature 256:495-497, the human B cell hybridoma technique (Kozbor et al. (1983) Immunol. Today 4:72), the EBV-hybridoma technique (Cole et al. (1985) in Monoclonal Antibodies and Cancer Therapy, ed. Reisfeld and Sell (Alan R. Liss, Inc., New York, N.Y.), pp. 77-96) or trioma techniques. The technology for producing hybridomas is well known (see generally Coligan et al., eds. (1994) Current Protocols in Immunology (John Wiley & Sons, Inc., New York, N.Y.); Galfre et al. (1977) Nature 266:550-52; Kenneth (1980) in Monoclonal Antibodies: A New Dimension In Biological Analyses (Plenum Publishing Corp., NY); and Lerner (1981) Yale J. Biol. Med., 54:387-402).
Alternative to preparing monoclonal antibody-secreting hybridomas, a monoclonal antibody can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with a biomarker protein to thereby isolate immunoglobulin library members that bind the biomarker protein. Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAP I Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, U.S. Pat. No. 5,223,409; PCT Publication Nos. WO 92/18619; WO 91/17271; WO 92/20791; WO 92/15679; 93/01288; WO 92/01047; 92/09690; and 90/02809; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse et al. (1989) Science 246:1275-1281; Griffiths et al. (1993) EMBO J. 12:725-734.
Detection of antibody binding can be facilitated by coupling the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin; and examples of suitable radioactive material include 125I, 131I, 35S, or 3H.
In regard to detection of antibody staining in the immunocytochemistry methods of the invention, there also exist in the art, video-microscopy and software methods for the quantitative determination of an amount of multiple molecular species (e.g., biomarker proteins) in a biological sample wherein each molecular species present is indicated by a representative dye marker having a specific color. Such methods are also known in the art as a colorimetric analysis methods. In these methods, video-microscopy is used to provide an image of the biological sample after it has been stained to visually indicate the presence of a particular biomarker of interest. Some of these methods, such as those disclosed in U.S. patent application Ser. No. 09/957,446 to Marcelpoil et al. and U.S. patent application Ser. No. 10/057,729 to Marcelpoil et al., incorporated herein by reference, disclose the use of an imaging system and associated software to determine the relative amounts of each molecular species present based on the presence of representative color dye markers as indicated by those color dye markers' optical density or transmittance value, respectively, as determined by an imaging system and associated software. These techniques provide quantitative determinations of the relative amounts of each molecular species in a stained biological sample using a single video image that is “deconstructed” into its component color parts.
The antibodies used to practice the invention are selected to have high specificity for the biomarker proteins of interest. Methods for making antibodies and for selecting appropriate antibodies are known in the art. See, for example, Celis, ed. (in press) Cell Biology & Laboratory Handbook, 3rd edition (Academic Press, New York), which is herein incorporated in its entirety by reference. In some embodiments, commercial antibodies directed to specific biomarker proteins may be used to practice the invention. The antibodies of the invention may be selected on the basis of desirable staining of cytological, rather than histological, samples. That is, in particular embodiments the antibodies are selected with the end sample type (i.e., cytology preparations) in mind and for binding specificity.
In some aspects of the invention, antibodies directed to specific biomarkers of interest are selected and purified via a multi-step screening process. In particular embodiments, polydomas are screened to identify biomarker-specific antibodies that possess the desired traits of specificity and sensitivity. As used herein, “polydoma” refers to multiple hybridomas. The polydomas of the invention are typically provided in multi-well tissue culture plates. In the initial antibody screening step, a tumor tissue microarray comprising multiple normal (i.e., no CIN), CINIII, squamous cell carcinoma, and adenocarcinoma samples is generated. Methods and equipment, such as the Chemicon® Advanced Tissue Arrayer, for generating arrays of multiple tissues on a single slide are known in the art. See, for example, U.S. Pat. No. 4,820,504. Undiluted supernatants from each well containing a polydoma are assayed for positive staining using standard immunohistochemistry techniques. At this initial screening step, background, non-specific binding is essentially ignored. Polydomas producing positive results are selected and used in the second phase of antibody screening.
In the second screening step, the positive polydomas are subjected to a limiting dilution process. The resulting unscreened antibodies are assayed for positive staining of CINIII or cervical carcinoma samples using standard immunohistochemistry techniques. At this stage, background staining is relevant, and the candidate polydomas that only stain positive for abnormal cells (i.e., CINIII and cancer cells) only are selected for further analysis.
To identify antibodies that can distinguish normal and CINI samples from those indicative of high-grade cervical disease (i.e., CINII and above), a disease panel tissue microarray is generated. This tissue microarray typically comprises multiple no CIN, CINI, CINII, CINIII, squamous cell carcinoma, and adenocarcinoma samples. Standard immunohistochemistry techniques are employed to assay the candidate polydomas for specific positive staining of samples indicative of high-grade cervical disease only (i.e., CINII samples and above). Polydomas producing positive results and minimal background staining are selected for further analysis.
Positive-staining cultures are prepared as individual clones in order to select individual candidate monoclonal antibodies. Methods for isolating individual clones are well known in the art. The supernatant from each clone comprising unpurified antibodies is assayed for specific staining of CINII, CINIII, squamous cell carcinoma, and adenocarcinoma samples using the tumor and disease panel tissue microarrays described herein above. Candidate antibodies showing positive staining of high-grade cervical disease samples (i.e., CINII and above), minimal staining of other cell types (i.e., normal and CINI samples), and little background are selected for purification and further analysis. Methods for purifying antibodies through affinity adsorption chromatography are well known in the art.
In order to identify antibodies that display maximal specific staining of high-grade cervical disease samples and minimal background, non-specific staining in cervical cytology samples, the candidate antibodies isolated and purified in the immunohistochemistry-based screening process above are assayed using the immunocytochemistry techniques of the present invention. Exemplary protocols for performing immunocytochemistry are provided in Examples 1 and 2.
Specifically, purified antibodies of interest are used to assay a statistically significant number of NIL (i.e., no invasive lesion), ASCUS, LSIL, HSIL or cancerous cervical cytology patient samples. The samples are analyzed by immunocytochemistry as described herein and classified as positive, negative, or indeterminate for high-grade cervical disease on the basis of positive antibody staining for a particular biomarker. Sensitivity, specificity, positive predictive values, and negative predictive values for each antibody are calculated. Antibodies exhibiting maximal specific staining of high-grade cervical disease in cervical cytology samples with minimal background (i.e., maximal signal to noise ratio) are selected for the present invention.
Identification of appropriate antibodies results in an increase in signal to noise ratio and an increase in the clinical utility of the assay. Assay format and sample type to be used are critical factors in selection of appropriate antibodies. Many antibodies directed to biomarkers do not produce a desirable signal to noise ratio in an immunocytochemistry format with cytology preparations or in an immunohistochemistry format with formalin-fixed paraffin-embedded samples. Moreover, biomarker antibodies that produce a maximal signal to noise ratio in an immunohistochemistry format may not work as well in immunocytochemistry assays. For example, an antibody that produces the desired level of staining in an immunocytochemistry format may not produce the appropriate level of staining in an immunohistochemistry assay (data not shown). Likewise, an antibody that produces an acceptable signal to noise ratio when used in the immunohistochemistry assay may result in overstaining of immunocytochemistry samples (data not shown). Thus, antibody selection requires early consideration of the assay format and the end sample type to be used.
Cytology-based assays (i.e., immunocytochemistry) differ from tissue-based assays (i.e., immunohistochemistry) insofar as the tissue architecture is not available to assist with staining interpretation in the immunocytochemistry format. For example, in an immunohistochemistry assay performed on samples from patients with mild dysplasia or squamous cell carcinoma with an antibody directed to Claudin 1, the results indicated that Claudin 1 was expressed in the lesion of the mild dysplasia sample (i.e., light brown staining) but was significantly overexpressed (i.e., dark brown staining) in the cancer lesion (FIG. 12). The results obtained with the same Claudin 1 antibody in an immunocytochemistry assay format were indeterminate (FIG. 13). While abnormal cells are easily detectable using a Claudin 1 antibody in an immunohistochemistry assay, the results obtained by the staining of Claudin 1 in the immunocytochemistry assay of the invention were more difficult to interpret. Therefore, biomarkers that are appropriate in an immunohistochemistry format may not be suitable in an immunocytochemistry assay and, thus, are not included in the preferred embodiment of the invention.
Furthermore, the location of biomarkers within the cell is also an important consideration in immunocytochemistry assays. Biomarkers that display nuclear, cytoplasmic, or membrane staining patterns can be confirmed morphologically and are appropriate for immunohistochemistry methods. Cytoplasmic and membrane staining, however, make it difficult to identify critical morphological characteristics of cervical disease (e.g., nuclear to cytoplasmic ratio) in immunocytochemistry assays. See FIG. 15. In contrast, biomarkers that are expressed in the nucleus and show a nuclear staining pattern facilitate detection of antibody staining and also permit morphological analysis. See FIG. 15. Thus, in some preferred embodiments, only biomarkers that are selectively expressed in the nucleus are used in an immunocytochemistry assay of the invention.
One of skill in the art will recognize that optimization of antibody titer and detection chemistry is needed to maximize the signal to noise ratio for a particular antibody. Antibody concentrations that maximize specific binding to the biomarkers of the invention and minimize non-specific binding (or “background”) will be determined. In particular embodiments, appropriate antibody titers for use in cervical cytology preparations are determined by initially testing various antibody dilutions on formalin-fixed paraffin-embedded normal and high-grade cervical disease tissue samples. Optimal antibody concentrations and detection chemistry conditions are first determined for formalin-fixed paraffin-embedded cervical tissue samples. The design of assays to optimize antibody titer and detection conditions is standard and well within the routine capabilities of those of ordinary skill in the art. After the optimal conditions for fixed tissue samples are determined, each antibody is then used in cervical cytology preparations under the same conditions. Some antibodies require additional optimization to reduce background staining and/or to increase specificity and sensitivity of staining in the cytology samples.
Furthermore, one of skill in the art will recognize that the concentration of a particular antibody used to practice the methods of the invention will vary depending on such factors as time for binding, level of specificity of the antibody for the biomarker protein, and method of body sample preparation. Moreover, when multiple antibodies are used, the required concentration may be affected by the order in which the antibodies are applied to the sample, i.e., simultaneously as a cocktail or sequentially as individual antibody reagents. Furthermore, the detection chemistry used to visualize antibody binding to a biomarker of interest must also be optimized to produce the desired signal to noise ratio.
In other embodiments, the expression of a biomarker of interest is detected at the nucleic acid level. Nucleic acid-based techniques for assessing expression are well known in the art and include, for example, determining the level of biomarker mRNA in a body sample. Many expression detection methods use isolated RNA. Any RNA isolation technique that does not select against the isolation of mRNA can be utilized for the purification of RNA from cervical cells (see, e.g., Ausubel et al., ed., (1987-1999) Current Protocols in Molecular Biology (John Wiley & Sons, New York). Additionally, large numbers of tissue samples can readily be processed using techniques well known to those of skill in the art, such as, for example, the single-step RNA isolation process of Chomczynski (1989, U.S. Pat. No. 4,843,155).
The term “probe” refers to any molecule that is capable of selectively binding to a specifically intended target biomolecule, for example, a nucleotide transcript or a protein encoded by or corresponding to a biomarker. Probes can be synthesized by one of skill in the art, or derived from appropriate biological preparations. Probes may be specifically designed to be labeled. Examples of molecules that can be utilized as probes include, but are not limited to, RNA, DNA, proteins, antibodies, and organic molecules.
Isolated mRNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or Northern analyses, polymerase chain reaction analyses and probe arrays. One method for the detection of mRNA levels involves contacting the isolated mRNA with a nucleic acid molecule (probe) that can hybridize to the mRNA encoded by the gene being detected. The nucleic acid probe can be, for example, a full-length cDNA, or a portion thereof, such as an oligonucleotide of at least 7, 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to an mRNA or genomic DNA encoding a biomarker of the present invention. Hybridization of an mRNA with the probe indicates that the biomarker in question is being expressed.
In one embodiment, the mRNA is immobilized on a solid surface and contacted with a probe, for example by running the isolated mRNA on an agarose gel and transferring the mRNA from the gel to a membrane, such as nitrocellulose. In an alternative embodiment, the probe(s) are immobilized on a solid surface and the mRNA is contacted with the probe(s), for example, in an Affymetrix gene chip array. A skilled artisan can readily adapt known mRNA detection methods for use in detecting the level of mRNA encoded by the biomarkers of the present invention.
An alternative method for determining the level of biomarker mRNA in a sample involves the process of nucleic acid amplification, e.g., by RT-PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA 88:189-193), self sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi et al. (1988) Bio/Technology 6:1197), rolling circle replication (Lizardi et al., U.S. Pat. No. 5,854,033) or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers. In particular aspects of the invention, biomarker expression is assessed by quantitative fluorogenic RT-PCR (i.e., the TaqMan® System). Such methods typically utilize pairs of oligonucleotide primers that are specific for the biomarker of interest. Methods for designing oligonucleotide primers specific for a known sequence are well known in the art.
Biomarker expression levels of RNA may be monitored using a membrane blot (such as used in hybridization analysis such as Northern, Southern, dot, and the like), or microwells, sample tubes, gels, beads or fibers (or any solid support comprising bound nucleic acids). See U.S. Pat. Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, which are incorporated herein by reference. The detection of biomarker expression may also comprise using nucleic acid probes in solution.
In one embodiment of the invention, microarrays are used to detect biomarker expression. Microarrays are particularly well suited for this purpose because of the reproducibility between different experiments. DNA microarrays provide one method for the simultaneous measurement of the expression levels of large numbers of genes. Each array consists of a reproducible pattern of capture probes attached to a solid support. Labeled RNA or DNA is hybridized to complementary probes on the array and then detected by laser scanning. Hybridization intensities for each probe on the array are determined and converted to a quantitative value representing relative gene expression levels. See, U.S. Pat. Nos. 6,040,138, 5,800,992 and 6,020,135, 6,033,860, and 6,344,316, which are incorporated herein by reference. High-density oligonucleotide arrays are particularly useful for determining the gene expression profile for a large number of RNA's in a sample.
Techniques for the synthesis of these arrays using mechanical synthesis methods are described in, e.g., U.S. Pat. No. 5,384,261, incorporated herein by reference in its entirety for all purposes. Although a planar array surface is preferred, the array may be fabricated on a surface of virtually any shape or even a multiplicity of surfaces. Arrays may be peptides or nucleic acids on beads, gels, polymeric surfaces, fibers such as fiber optics, glass or any other appropriate substrate, see U.S. Pat. Nos. 5,770,358, 5,789,162, 5,708,153, 6,040,193 and 5,800,992, each of which is hereby incorporated in its entirety for all purposes. Arrays may be packaged in such a manner as to allow for diagnostics or other manipulation of an all-inclusive device. See, for example, U.S. Pat. Nos. 5,856,174 and 5,922,591 herein incorporated by reference.
In one approach, total mRNA isolated from the sample is converted to labeled cRNA and then hybridized to an oligonucleotide array. Each sample is hybridized to a separate array. Relative transcript levels may be calculated by reference to appropriate controls present on the array and in the sample.
Kits for practicing the methods of the invention are further provided. By “kit” is intended any manufacture (e.g., a package or a container) comprising at least one reagent, e.g., an antibody, a nucleic acid probe, etc. for specifically detecting the expression of a biomarker of the invention. The kit may be promoted, distributed, or sold as a unit for performing the methods of the present invention. Additionally, the kits may contain a package insert describing the kit and methods for its use.
In a particular embodiment, kits for practicing the immunocytochemistry methods of the invention are provided. Such kits are compatible with both manual and automated immunocytochemistry techniques (e.g., cell staining) as described below in Example 1. These kits comprise at least one antibody directed to a biomarker of interest, chemicals for the detection of antibody binding to the biomarker, a counterstain, and, optionally, a bluing agent to facilitate identification of positive staining cells. Any chemicals that detect antigen-antibody binding may be used in the practice of the invention. In some embodiments, the detection chemicals comprise a labeled polymer conjugated to a secondary antibody. For example, a secondary antibody that is conjugated to an enzyme that catalyzes the deposition of a chromogen at the antigen-antibody binding site may be provided. Such enzymes and techniques for using them in the detection of antibody binding are well known in the art. In one embodiment, the kit comprises a secondary antibody that is conjugated to an HRP-labeled polymer. Chromogens compatible with the conjugated enzyme (e.g., DAB in the case of an HRP-labeled secondary antibody) and solutions, such as hydrogen peroxide, for blocking non-specific staining may be further provided. In other embodiments, antibody binding to a biomarker protein is detected through the use of a mouse probe reagent that binds to mouse monoclonal antibodies, followed by addition of a dextran polymer conjugated with HRP that binds to the mouse probe reagent. Such detection reagents are commercially available from, for example, Biocare Medical.
The kits of the present invention may further comprise a peroxidase blocking reagent (e.g., hydrogen peroxide), a protein blocking reagent (e.g., purified casein), and a counterstain (e.g., hematoxylin). A bluing agent (e.g., ammonium hydroxide or TBS, pH 7.4, with Tween-20 and sodium azide) may be further provided in the kit to facilitate detection of positive staining cells.
In another embodiment, the immunocytochemistry kits of the invention additionally comprise at least two reagents, e.g., antibodies, for specifically detecting the expression of at least two distinct biomarkers. Each antibody may be provided in the kit as an individual reagent or, alternatively, as an antibody cocktail comprising all of the antibodies directed to the different biomarkers of interest. Furthermore, any or all of the kit reagents may be provided within containers that protect them from the external environment, such as in sealed containers. An exemplary kit for practicing the methods of the invention is described below in Example 8.
Positive and/or negative controls may be included in the kits to validate the activity and correct usage of reagents employed in accordance with the invention. Controls may include samples, such as tissue sections, cells fixed on glass slides, etc., known to be either positive or negative for the presence of the biomarker of interest. In a particular embodiment, the positive control comprises SiHa cells. This is a human cervical squamous cancer cell line that is hypertriploid and positive for HPV-16 infection and, therefore, serves as a positive control for the overexpression of biomarkers in high-grade cervical disease states. SiHa control cells may be provided in the kits of the invention as prepared slides or as a cell suspension that is compatible with slide preparation. The design and use of controls is standard and well within the routine capabilities of those of ordinary skill in the art.
In other embodiments, kits for identifying high-grade cervical comprising detecting biomarker overexpression at the nucleic acid level are further provided. Such kits comprise, for example, at least one nucleic acid probe that specifically binds to a biomarker nucleic acid or fragment thereof. In particular embodiments, the kits comprise at least two nucleic acid probes that hybridize with distinct biomarker nucleic acids.
In some embodiments, the methods of the invention can be used in combination with traditional cytology techniques that analyze morphological characteristics. For example, the immunocytochemical techniques of the present invention can be combined with the conventional Pap stain so that all the morphological information from the conventional method is conserved. In this manner the detection of biomarkers can reduce the high false-negative rate of the Pap smear test and may facilitate mass automated screening. In a particular embodiment, the immunocytochemistry methods disclosed herein above are combined with the conventional Pap stain in a single method, as described below in Example 6-7. A combined immunocytochemistry and Pap staining method permits visualization of both biomarkers that are selectively overexpressed in high-grade cervical disease and cell morphology in a single sample (e.g., a microscope slide comprising a monolayer of cervical cells). The combined immunocytochemistry and Pap staining method may permit the more accurate identification and diagnosis of high-grade cervical disease, particularly in cases mistakenly classified as normal, LSIL, or ASCUS by conventional Pap testing. Analysis of both biomarker overexpression and cell morphology in a single method could replace the Pap smear as the primary screening method for cervical cancer.
One of skill in the art will recognize that the staining parameters (e.g., incubation times, wash conditions, chromogen/stain concentrations, etc.) for this combined methodology will need to be optimized such that a sufficient contrast between the immunocytochemistry output (e.g., chromogen staining) and the Pap stain is obtained. The design of assays to optimize staining parameters is standard and well within the routine capabilities of those of ordinary skill in the art. Kits for performing the combined immunocytochemistry and Pap staining method are also encompassed by the present invention. Such kits comprise the reagents needed for immunocytochemistry, as described herein above, and the reagents for conventional Pap staining, particularly EA50 and Orange G.
One of skill in the art will further appreciate that any or all steps in the methods of the invention could be implemented by personnel or, alternatively, performed in an automated fashion. Thus, the steps of body sample preparation, sample staining, and detection of biomarker expression may be automated.
The following examples are offered by way of illustration and not by way of limitation:
EXPERIMENTAL
Example 1
Detection of Biomarker Overexpression Using Immunocytochemistry
Slide Preparation and Pretreatment
Patient cervical samples are collected and placed into a SurePathTM collection vial (TriPath Imaging, Inc.). Cervical cells are collected from the liquid medium and deposited in a thin layer on a glass slide using the PrepStainTM slide processor system (TriPath Imaging, Inc.). Prepared slides are immediately transferred to a pretreatment buffer (1% RAM) and heated for 45 minutes at 95° C. The slides are cooled to room temperature and rinsed three times (2 minutes per rinse) in TBS (tris buffered saline).
Manual Immunocytochemistry
To prevent non-specific background staining, slides are not permitted to dry out during the staining procedure. Furthermore, in order to block non-specific staining, hydrogen peroxide is applied to the slides for 5 minutes, followed by a TBS rinse. An antibody directed to MCM6 is applied to the slide for 1 hour at room temperature. Following incubation with the MCM6 antibody, the slide is washed three times with TBS for 2 minutes per wash. The Dako Envision+ HRP-labeled polymer secondary antibody is applied to the slide for 30 minutes at room temperature, followed by a TBS rinse. The HRP substrate chromogen DAB is applied for 10 minutes, and then the slides are rinsed for 5 minutes with water. Each slide is counterstained with hematoxylin and then rinsed with water until clear. Following counterstaining, the slides are soaked in ammonium hydroxide for 10 seconds and then rinsed with water for 1 minute.
Samples are dehydrated by immersing the slides in 95% ethanol for 1 minute and then in absolute ethanol for an additional minute. Slides are cleared by rinsing 3 times in xylene for 1 minute per rinse. Slides are then coverslipped with permanent mounting media and incubated at 35° C. to dry. Positive staining cells are visualized using a bright-field microscope.
Automated Immunocytochemistry
The Dako Autostainer Universal Staining system is programmed according to the manufacturer's instructions, and the necessary staining and counterstaining reagents described above for manual immunocytochemistry are loaded onto the machine. The prepared and pretreated slides are loaded onto the Autostainer, and the program is run. At the end of the run, the slides are removed and rinsed in water for 5 minutes. The slides are dehydrated, cleared, coverslipped, and analyzed as described above.
Example 2
Detection of Biomarkers in Clinical Samples
Approximately 180 cervical cytology patient samples representing various diagnoses were collected. The presence or absence of cancerous cells or lesions indicative of high-grade disease in these patients was previously confirmed by colposcopy. The following table indicates the number of samples within each diagnosis group analyzed in this study, as well as a description of the colposcopy findings (e.g., presence or absence of high-grade lesions).







TABLE 1







Specimens analyzed











Diagnosis
Count
Description







NIL
72
HPV Negative



ASC-US
26
26 without lesion





 0 with lesion or high risk HPV



LSIL
48
42 negative for high grade lesion





 6 positive for high grade lesion



HSIL
25



Cancer
10
Squamous Cell Carcinoma and





Adenocarcinoma










The samples were analyzed by immunocytochemistry methods to identify high-grade cervical disease. Antibodies were used to detect the overexpression of six biomarkers of interest: MCM2, MCM6, MCM 7, p21waf1, Cyclin E, and Topo2A. Assay controls included MCM2, MCM6, MCM7, p21waf1, Cyclin E, Topo2A and a mouse IgG negative run on the SiHa cell line. Samples were also analyzed by traditional Pap staining techniques.
Preparation of Slides
Each sample was removed from storage and allowed to come to room temperature. 6 ml of TriPath CytoRich® preservative was added to each vial, and the vials were vortexed. Samples were processed on the TriPath PrepMate® automated processor, and any remaining fluid in the vial was transferred to a centrifuge tube. The samples were centrifuged for 2 minutes at 200× g, and the supernatant was aspirated. The samples were then centrifuged for 10 minutes at 800× g, and the supernatant was decanted. Sample tubes were loaded onto the TriPath PrepStain® system and the system software (version 1.1; Transfer Only) was run. Eight slides for each patient sample were prepared and stored in 95% ethanol for at least 24 hours but not longer than 2 weeks prior to use in Pap staining and immuocytochemistry methods.
Pap Staining Method
Prepared slides were incubated in 95% ethanol for 30 seconds and then rinsed with water for an additional 30 seconds. Hematoxylin was applied to the slides for 6 minutes. Slides were rinsed in water for 1 minute, acid water for 2 seconds, and water for 30 seconds. A bluing agent (ammonium hydroxide) was applied for 30 seconds, and the slides were rinsed first in water and then in 95% ethanol for 30 seconds each. EA 50 and Orange G (Autocyte®) were applied for 6 minutes. The slides were rinsed 2 times in 95% ethanol, 3 times in 100% ethanol, and 3 times in xylene for 30 seconds per rinse.
The slides were then coverslipped using Acrytol mounting media and incubated at 35° C. to dry. Samples were reviewed by a pathologist using a bright-field microscope.
Immunocytochemistry Method
Prepared slides were removed from the 95% ethanol and rinsed with deionized water for approximately 1 minute. Slides were placed in a 1× Target Retrieval Solution pH 6.0 (DAKO S1699)/dH20 bath preheated to 95° C. and placed in a steamer for 25 minutes. Samples were allowed to cool for 20 minutes at room temperature, rinsed well in deionized water, and placed in TBS. Pretreated slides were stained for biomarker expression essentially as described above in Example 1, “Automated Immunocytochemistry.” Commercial antibodies directed to MCM2 (1:200), MCM7 (1:25), p21waf1 (1:100), and cylcin E (1:100) were diluted as indicated and used to detect biomarker expression. Purified MCM6 antibody, identified by polydoma screening as described in Example 4, was used at a 1:6000 dilution.
Interpretation of Slides
Each slide was screened and reviewed by a cytotechnologist and a pathologist. Samples were classified as positive, negative, or indeterminate for high-grade cervical disease according to the following parameters:

    
    
        Non-cellular artifacts and inflammatory cells staining brown (DAB) were disregarded.
        Mature, normal-appearing squamous cells and normal-appearing glandular cells were not counted as positive when staining with DAB.
        Squamous metaplastic cells along with abnormal cells were considered positive.
        A staining intensity of less than 1.5 was considered negative.
        Discrepant results were resolved through joint review of slides.
    
    


The immunocytochemistry results were compared with the results previously obtained by colposcopy. Each slide was then given a final result of true positive (TP), true negative (TN), false positive (FP), false negative (FN), or indeterminate. Sensitivity, specificity, positive predictive values, and negative predictive values for each biomarker were calculated.
Results
The results for each biomarker are summarized below.







TABLE 2







MCM2














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
71
1
72


ASC-US (No Lesion)
0
0
0
25
1
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
7
0
31
4
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
24
0
1
0
0
25


Cancer
7
0
1
0
2
10



34
7
5
127
8
181












Sensitivity
0.8718



Specificity
0.9478


PPV
0.8293


NPV
0.9621













TABLE 3







MCM6














TP
FP
FN
TN
Indeter.
Totals
















NIL
0
0
0
68
4
72


ASC-US (No Lesion)
0
3
0
22
1
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
14
0
24
4
42


LSIL (HSIL)
3
0
2
0
1
6


HSIL
22
0
0
0
3
25


Cancer
10
0
0
0
0
10



35
17
2
114
13
181












Sensitivity
0.9459



Specificity
0.8702


PPV
0.6731


NPV
0.9828













TABLE 4







MCM7














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
67
5
72


ASC-US (No Lesion)
0
2
0
21
3
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
12
0
28
2
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
1
0
0
25


Cancer
9
0
0
0
1
10



37
14
3
116
11
181












Sensitivity
0.9250



Specificity
0.8923


PPV
0.7255


NPV
0.9748













TABLE 5







Cyclin E














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
72
0
72


ASC-US (No Lesion)
0
0
0
26
0
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
3
0
35
4
42


LSIL (HSIL)
2
0
4
0
0
6


HSIL
15
0
4
0
6
25


Cancer
7
0
2
0
1
10



24
3
10
133
11
181












Sensitivity
0.7059



Specificity
0.9779


PPV
0.8889


NPV
0.9301













TABLE 6







p21waf1














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
61
9
72


ASC-US (No Lesion)
0
1
0
22
3
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
12
0
23
7
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
21
0
1
0
3
25


Cancer
7
0
2
0
1
10



31
15
6
106
23
181












Sensitivity
0.8378



Specificity
0.8760


PPV
0.6739


NPV
0.9464













TABLE 7







TOPO2A














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
68
4
72


ASC-US (No Lesion)
0
1
0
24
1
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
4
0
27
11
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
21
0
1
0
3
25


Cancer
9
0
0
0
1
10



33
5
4
119
20
181












Sensitivity
0.8919



Specificity
0.9597


PPV
0.8684


NPV
0.9675






Approximately 180 cases were analyzed for the presence of high-grade cervical disease using the immunocytochemistry methods of the invention. Of that number, the MCM biomarkers produced an indeterminate rate ranging from 4% to 7%. Additionally, MCM2 showed a specificity of 95% with a sensitivity of 87%. The MCM6 and MCM7 biomarkers produced comparable sensitivity results of 95% and 93%, respectively. The specificity for these two biomarkers ranged from 87% to 89%.
Cyclin E produced the highest specificity value of 98%. Although the indeterminate rate was 6%, the sensitivity was only 71%. The indeterminate rate for p21waf1 was the highest of all markers tested at 13%. p21waf1 produced a sensitivity of 84% and a specificity of 88%. 96% specificity was observed with the biomarker Topo2A. The indeterminate rate for Topo2A was 11%, with a sensitivity of 89%.
Example 3
Detection of Biomarkers in Clinical Samples Using Antibody Cocktails
Approximately 180 colposcopy-confirmed cervical cytology samples were analyzed by immunocytochemistry methods to identify high-grade cervical disease. Each sample was analyzed for the expression of multiple biomarkers of interest. Specifically, various combinations of antibodies directed to MCM2, MCM6, MCM 7, p21waf1, Cyclin E, and Topo2A were analyzed for their ability to detect high-grade cervical disease. These samples were evaluated for the expression of multiple biomarkers of interest using the immunocytochemistry methods and slide interpretation guidelines described in Example 2.
The immunocytochemistry results were compared with the results previously obtained by colposcopy. Each slide was then given a final result of true positive (TP), true negative (TN), false positive (FP), false negative (FN), or indeterminate. Sensitivity, specificity, positive predictive values, and negative predictive values for each biomarker were calculated.
Results
The results for each biomarker are summarized below.







TABLE 8







MCM2 and MCM7














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
66
6
72


ASC-US (No Lesion)
0
2
0
20
4
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
13
0
25
4
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
1
0
0
25


Cancer
10
0
0
0
0
10



38
15
3
111
14
181












Sensitivity
0.9268



Specificity
0.8810


PPV
0.7170


NPV
0.9737













TABLE 9







MCM6 and MCM7














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
65
7
72


ASC-US (No Lesion)
0
3
0
21
2
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
16
0
23
3
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
0
0
1
25


Cancer
10
0
0
0
0
10



38
19
2
109
13
181












Sensitivity
0.9500



Specificity
0.8516


PPV
0.6667


NPV
0.9820













TABLE 10







MCM7 and TOPO2A














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
64
8
72


ASC-US (No Lesion)
0
2
0
21
3
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
12
0
29
1
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
20
0
2
0
3
25


Cancer
8
0
0
0
2
10



32
14
4
114
17
181












Sensitivity
0.8889



Specificity
0.8906


PPV
0.6957


NPV
0.9661













TABLE 11







MCM7 and Cyclin E














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
67
5
72


ASC-US (No Lesion)
0
2
0
21
3
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
12
0
28
2
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
1
0
0
25


Cancer
10
0
0
0
0
10



38
14
3
116
10
181












Sensitivity
0.9268



Specificity
0.8923


PPV
0.7308


NPV
0.9748













TABLE 12







MCM7 and p21waf1














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
57
13
72


ASC-US (No Lesion)
0
3
0
20
3
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
14
0
21
7
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
1
0
0
25


Cancer
9
0
0
0
1
10



37
19
3
98
24
181





Sensitivity 0.9250


Specificity 0.8376


PPV 0.6607


NPV 0.9703













TABLE 13







MCM2 and MCM6














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
67
5
72


ASC-US (No Lesion)
0
3
0
21
2
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
17
0
21
4
42


LSIL (HSIL)
3
0
2
0
1
6


HSIL
24
0
0
0
1
25


Cancer
10
0
0
0
0
10



37
20
2
109
13
181





Sensitivity 0.9487


Specificity 0.8450


PPV 0.6491


NPV 0.9820













TABLE 14







MCM2 and TOPOIIA














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
67
5
72


ASC-US (No Lesion)
0
1
0
23
2
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
8
4
18
12
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
25
0
0
0
0
25


Cancer
9
0
0
0
1
10



37
9
7
108
20
181





Sensitivity 0.8409


Specificity 0.9231


PPV 0.8043


NPV 0.9391













TABLE 15







MCM2 and Cyclin E














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
71
1
72


ASC-US (No Lesion)
0
0
0
25
1
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
9
0
27
6
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
24
0
1
0
0
25


Cancer
8
0
2
0
0
10



35
9
6
123
8
181





Sensitivity 0.8537


Specificity 0.9318


PPV 0.7955


NPV 0.9535













TABLE 16







MCM2 and p21waf1














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
60
10
72


ASC-US (No Lesion)
0
1
0
21
4
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
13
0
21
8
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
24
0
1
0
0
25


Cancer
9
0
1
0
0
10



36
16
5
102
22
181





Sensitivity 0.8780


Specificity 0.8644


PPV 0.6923


NPV 0.9533













TABLE 17







TOPO2A and Cyclin E














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
68
4
72


ASC-US (No Lesion)
0
1
0
24
1
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
5
0
27
10
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
22
0
1
0
2
25


Cancer
9
0
0
0
1
10



34
6
4
119
18
181





Sensitivity 0.8947


Specificity 0.9520


PPV 0.8500


NPV 0.9675













TABLE 18







TOPO2A and p21waf1














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
58
12
72


ASC-US (No Lesion)
0
2
0
21
3
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
13
0
19
10
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
25
0
0
0
0
25


Cancer
10
0
0
0
0
10



38
17
3
98
25
181





Sensitivity 0.9268


specificity 0.8522


PPV 0.6909


NPV 0.9703













TABLE 19







p21waf1 and Cyclin E














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
61
9
72


ASC-US (No Lesion)
0
1
0
22
3
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
12
0
23
7
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
22
0
1
0
2
25


Cancer
8
0
1
0
1
10



33
15
5
106
22
181





Sensitivity 0.8684


Specificity 0.8760


PPV 0.6875


NPV 0.9550













TABLE 20







MCM2, MCM6, and MCM7














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
64
8
72


ASC-US (No Lesion)
0
3
0
20
3
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
17
0
21
4
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
0
0
1
25


Cancer
10
0
0
0
0
10



38
20
2
105
16
181





Sensitivity 0.9500


Specificity 0.8400


PPV 0.6552


NPV 0.9813













TABLE 21







MCM2, MCM7, and TOPO2A














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
63
9
72


ASC-US (No Lesion)
0
2
0
20
4
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
13
0
21
8
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
25
0
0
0
0
25


Cancer
10
0
0
0
0
10



39
15
2
104
21
181





Sensitivity 0.9512


Specificity 0.8739


PPV 0.7222


NPV 0.9811













TABLE 22







MCM6, MCM7, and TOPO2A














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
63
9
72


ASC-US (No Lesion)
0
3
0
21
2
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
16
0
20
6
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
25
0
0
0
0
25


Cancer
10
0
0
0
0
10



39
19
2
104
17
181





Sensitivity 0.9512


Specificity 0.8455


PPV 0.6724


NPV 0.9811













TABLE 23







MCM6, MCM7, and Cyclin E














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
65
7
72


ASC-US (No Lesion)
0
3
0
21
2
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
16
0
23
3
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
0
0
1
25


Cancer
10
0
0
0
0
10



38
19
2
109
13
181





Sensitivity 0.9500


Specificity 0.8516


PPV 0.6667


NPV 0.9820













TABLE 24







MCM2, MCM7, and Cyclin E














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
66
6
72


ASC-US (No Lesion)
0
2
0
20
4
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
13
0
25
4
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
1
0
0
25


Cancer
10
0
0
0
0
10



38
15
3
111
14
181





Sensitivity 0.9268


Specificity 0.8810


PPV 0.7170


NPV 0.9737













TABLE 25







MCM2, MCM7, and p21waf1














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
56
14
72


ASC-US (No Lesion)
0
3
0
18
5
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
14
0
20
8
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
1
0
0
25


Cancer
10
0
0
0
0
10



38
19
3
94
27
181





Sensitivity 0.9268


Specificity 0.8319


PPV 0.6667


NPV 0.9691













TABLE 26







MCM2, TOPOIIA and Cyclin E














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
67
5
72


ASC-US (No Lesion)
0
1
0
23
2
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
9
0
22
11
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
25
0
0
0
0
25


Cancer
9
0
0
0
1
10



37
10
3
112
19
181





Sensitivity 0.9250


Specificity 0.9180


PPV 0.7872


NPV 0.9739













TABLE 27







MCM2, Cyclin E and p21waf1














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
60
10
72


ASC-US (No Lesion)
0
1
0
21
4
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
13
0
21
8
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
24
0
1
0
0
25


Cancer
9
0
1
0
0
10



36
16
5
102
22
181





Sensitivity 0.8780


Specificity 0.8644


PPV 0.6923


NPV 0.9533













TABLE 28







MCM2, TOPOIIA and p21waf1














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
57
13
72


ASC-US (No Lesion)
0
2
0
20
4
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
13
0
18
11
42


LSIL (HSIL)
3
0
3
0
0
6


HSIL
25
0
0
0
0
25


Cancer
10
0
0
0
0
10



38
17
3
95
28
181





Sensitivity 0.9268


Specificity 0.8482


PPV 0.6909


NPV 0.9694













TABLE 29







MCM7, TOPO2A, and Cyclin E














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
64
8
72


ASC-US (No Lesion)
0
2
0
21
3
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
12
0
23
7
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
25
0
0
0
0
25


Cancer
10
0
0
0
0
10



39
14
2
108
18
181





Sensitivity 0.9512


Specificity 0.8852


PPV 0.7358


NPV 0.9818













TABLE 30







MCM7, p21waf1, and Cyclin E














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
57
13
72


ASC-US (No Lesion)
0
3
0
19
4
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
14
0
21
7
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
1
0
0
25


Cancer
10
0
0
0
0
10



38
19
3
97
24
181





Sensitivity 0.9268


Specificity 0.8362


PPV 0.6667


NPV 0.9700













TABLE 31







MCM7, p21waf1, and TOPO2A














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
54
16
72


ASC-US (No Lesion)
0
3
0
19
4
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
14
0
18
10
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
25
0
0
0
0
25


Cancer
10
0
0
0
0
10



39
19
2
91
30
181





Sensitivity 0.9512


Specificity 0.8273


PPV 0.6724


NPV 0.9785













TABLE 32







MCM2, MCM7, Cyclin E, and p21waf1














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
56
14
72


ASC-US (No Lesion)
0
3
0
18
5
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
14
0
20
8
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
24
0
1
0
0
25


Cancer
10
0
0
0
0
10



38
19
3
94
27
181





Sensitivity 0.9268


Specificity 0.8319


PPV 0.6667


NPV 0.9691













TABLE 33







MCM2, MCM7, Cyclin E and TOPOIIA














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
0
0
63
9
72


ASC-US (No Lesion)
0
2
0
20
4
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
13
0
21
8
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
25
0
0
0
0
25


Cancer
10
0
0
0
0
10



39
15
2
104
21
181





Sensitivity 0.9512


Specificity 0.8739


PPV 0.7222


NPV 0.9811













TABLE 34







MCM2, MCM7, Cyclin E, p21waf1, and TOPO2A














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
53
17
72


ASC-US (No Lesion)
0
3
0
18
5
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
14
0
18
10
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
25
0
0
0
0
25


Cancer
10
0
0
0
0
10



39
19
2
89
32
181





Sensitivity 0.9512


Specificity 0.8241


PPV 0.6724


NPV 0.9780













TABLE 35







MCM2, MCM6, MCM7, TOPO2A, Cyclin E, and p21waf1














TP
FP
FN
TN
Indeter.
Totals

















NIL
0
2
0
52
18
72


ASC-US (No Lesion)
0
4
0
18
4
26


ASC-US (Lesion)
0
0
0
0
0
0


LSIL (No HSIL)
0
18
0
16
8
42


LSIL (HSIL)
4
0
2
0
0
6


HSIL
25
0
0
0
0
25


Cancer
10
0
0
0
0
10



39
24
2
86
30
181





Sensitivity 0.9512


Specificity 0.7818


PPV 0.6190


NPV 0.9773






Data was compiled on 28 antibody cocktails, as described above. Biomarker expression was analyzed using cocktails comprising antibodies directed to 2, 3, 4, 5 or even all 6 of the biomarkers of interest. Twenty-one of the 28 antibody cocktails showed sensitivities greater than 92%. Four of the 28 cocktails produced specificities above 90% with the lowest value at 78%. The highest values were achieved with a combination of MCM2, TOPOIIA and Cyclin E. This cocktail yielded a sensitivity of 93% along with a specificity of 92%. It appears that a combination of at least 3 biomarkers should yield a sensitivity greater than 90%. It is recognized that adjustments to the assay would further increase the sensitivity and specificity of the assay.
Example 4
Detection of Biomarker Expression Using Antibody Cocktails
Antibody cocktails were prepared using various combinations of antibodies directed to Cyclin E, MCM2, MCM6, MCM7, p21waf1, and TOPO2a. The composition of each cocktail is listed in the table below.







TABLE 36







Composition of Antibody Cocktails










Cocktail ID
Biomarkers







Cocktail 1
Cyclin E, MCM2, MCM7



Cocktail 2
Cyclin E, MCM6, MCM7



Cocktail 3
Cyclin E, MCM7, p21waf1



Cocktail 4
Cyclin E, MCM7, TOPO2a



Cocktail 5
MCM2, MCM7, p21waf1



Cocktail 6
MCM6, MCM7, p21waf1



Cocktail 7
MCM7, p21waf1, TOPO2a



Cocktail 8
MCM2, MCM7, TOPO2a



Cocktail 9
MCM6, MCM7, TOPO2a



Cocktail 10
MCM2, MCM6, MCM7



Cocktail 11
Cyclin E, MCM2, MCM6, MCM7, p21waf1,




TOPO2a



Cocktail 12
Cyclin E, MCM2, MCM7, p21waf1



Cocktail 13
MCM2 and MCM 7



Cocktail 14
MCM7 and p21waf1



Cocktail 15
MCM7 and Cyclin E



Cocktail 16
MCM2 and p21waf1



Cocktail 17
Cyclin E and p21waf1



Cocktail 18
MCM2 and Cyclin E



Cocktail 19
MCM7 and TOPO2a



Cocktail 20
MCM2 and TOPO2a



Cocktail 21
Cyclin E and TOPO2a



Cocktail 22
p21waf1 and TOPO2a










Two sets of cervical cytology specimens were prepared by pooling HSIL cases (HSIL pool) and NIL cases (NIL pool). Each antibody cocktail was then tested on the HSIL pool and the NIL pool. Biomarker antibodies were also tested individually as a control. Slide preparation and automated immunocytochemistry were performed as described in Example 2.
Slides were screened and reviewed by a cytotechnologist and a pathologist. Specific staining of cells indicative of high-grade cervical disease, staining of glandular cells, bacteria cross-reactivity, and the location of cell staining were all variables that were recorded during the screening process.
The immunocytochemistry results indicated an increase in staining of cells indicative of high-grade cervical disease in the HSIL pool with the biomarker antibody cocktails when compared to the results obtained with detection of a single biomarker. Additionally, there was no significant increase in background when the number of antibodies in the cocktails increased from 2 to 3, 4 or 6. Furthermore, the various antibody cocktails did not show an increase in background staining when tested on the NIL pool.
Example 5
Detection of Biomarker Overexpression in Cervical Samples Using Immunocytochemistry
Slide Preparation and Pretreatment
Patient cervical samples were collected as described above in Example 1. Slides comprising a monolayer of cervical cells were prepared by the AutoPrep® System using “prep only” mode. Prepared slides were immediately placed in 1× SureSlide® Pretreatment Buffer (0.5% sodium laureth-13-carboxylate (Sandopan LS) in deionized H20) for a minimum of 1 hour and a maximum of 72 hours. The pretreated slides were placed in a steamer at 95° C. for 45 minutes without preheating. Slides were removed from the steamer, allowed to cool at room temperature for 20 minutes, and then rinsed well in deionized water. Slides were rinsed in TBST (TBS/Tween-20) twice at 2 minutes per rinse. The slides were tapped to remove excess buffer and placed into a humid chamber. Slides were subjected to manual or automated immunocytochemistry, as described below.
Manual Immunocytochemistry
200 μl of peroxidase block reagent (0.03% hydrogen peroxide) was applied to each slide to cover the cell deposition area for a period of 5 minutes. The slides were then rinsed with TBST three times at 2 minutes per rinse. Excess buffer was removed, and the slides were placed into a humid chamber. 200 μl of protein block reagent (purified casein and surfactant) was applied to each slide and incubated for 5 minutes. After the excess protein block reagent was removed, the slides were placed in a humid chamber.
200 μl of primary monoclonal antibody cocktail comprising two mouse anti-human antibodies directed to MCM2 (clone 27C5.6 at 0.39 mg/ml, 1:800 dilution; clone 26H6.19 at 0.918 mg/ml, 1:10,000 dilution) and a third mouse anti-human antibody specific for Topo2A (clone SWT3D1 at 100 μg/ml, 1:10,000 dilution) was applied to each slide to completely cover the cell deposition area. Slides were incubated for 30 minutes and then rinsed with TBST three times at 2 minutes per rinse. Excess buffer was removed, and the slides were returned to the humid chamber. 200 μl of mouse probe reagent that binds to mouse monoclonal antibodies was applied as above for 20 minutes. The slides were rinsed with TBST three times at 2 minutes per rinse. Excess buffer was removed, and the slides were again placed into the humid chamber.
200 μl of polymer reagent comprising a dextran polymer conjugated with HRP and a secondary goat anti-mouse antibody that binds to the mouse probe reagent was applied as above for 20 minutes and then the slides rinsed with TBST 3 times at 2 minutes per rinse. After the excess buffer was removed, the slides were returned to the humid chamber. 200 μl of DAB substrate-chromgen solution was applied as above for 5 minutes. The slides were rinsed with deionized water for 5 minutes and then rinsed with TBST for 2 minutes with one change of buffer. Excess buffer was removed and the slides were placed in a humid chamber as before. 200 μl of hematoxylin was added for 1 minute, followed by 3 rinses with deionized water at 2 minutes per rinse. Excess deionized water was removed, and the slides were placed into the humid chamber. 200 μl of bluing agent (i.e., TBS, pH 7.4 with tween-20 and sodium azide) was applied to each slide for 1 minute. The slides were then rinsed in one change of TBST and 1 change of deionized water for 2 minutes each. The slides were then dehydrated, cleared, coverslipped, and analyzed as described in Examples 1 and 2.
Automated Immunocytochemistry
The autostainer was programmed according to manufacturer's instructions to include the following sequence of steps:

    
    
        a. 2 buffer rinses (TBST)
        b. 5 min peroxidase block
        c. 2 buffer rinses (TBST)
        d. 5 min protein block, blow
        e. 30 min primary antibody cocktail incubation
        f. 3 buffer rinses (TBST)
        g. 20 min mouse probe reagent
        h. 3 buffer rinses (TBST)
        i. 20 min polymer-HRP
        j. 3 buffer rinses (TBST)
        k. 5 min DAB (1 drop of chromagen to 1 ml of buffer)
        l. 3H2O rinses
        m. 2 buffer rinses (TBST)
        n. 1 min Mayer's hematoxylin
        o. 3H2O rinses
        p. 1 min bluing agent
        q. 1 buffer rinse (TBST)
        r. 1H2O rinse
    
    


The necessary staining and counterstaining reagents were loaded onto the machine. The prepared and pretreated slides were loaded onto the autostainer, and the above program was run. At the end of the run, the slides were removed and rinsed briefly in tap water. The slides were dehydrated, cleared, coverslipped, and analyzed as described in Examples 1 and 2.
Results







TABLE 37





NIL Cases (n = 45)







Pap Result









NIL
Other
Unsatisfactory





44
1 (ASC-US)
0










ICC Result









Positive
Negative
Unsatisfactory





 0
44
1
















TABLE 38





HSIL Cases (n = 45)







Pap Result









HSIL
Other
Unsatisfactory





45
0
0










ICC Result









Positive
Negative
Unsatisfactory





45
0
0









Of the 45 NIL cases tested, a review of the Pap stained slides revealed one ASC-US case. The immunocytochemistry (ICC) results for the NIL samples were negative, with one case deemed unsatisfactory for evaluation. Regarding the HSIL cases, each of the 45 cases was confirmed to be high-grade cervical disease based upon the review of the Pap stained slides. Additionally, each of the 45 HSIL cases was also positive in the ICC assay. The negative control, i.e., a universal mouse IgG control applied to the SiHa cell line control, produced negative results in the ICC assay. The positive control, i.e., the primary antibody cocktail applied to the SiHa cell line control, produced positive results in the ICC assay.
Example 6
Combined Immunocytochemistry and Pap Staining Procedure
Patient cervical samples were collected as described above in Example 1. Slides comprising a monolayer of cervical cells were prepared and pretreated as indicated in Example 5. Each pretreated slide was subjected to automated immunocytochemistry and Pap staining, thereby permitting visualization of both biomarker overexpression and cell morphology on a single slide.
Automated Immunocytochemistry
Automated immunocytochemistry was performed on each slide as described above in Example 5. At the end of the staining program, the slides were removed from the autostainer and rinsed in tap water for 3-5 minutes. Each slide was then stained according to conventional Pap staining methods, as described below.
Pap Staining Method
Following automated immunocytochemistry, each slide was further stained with Pap stain. The slides were first rinsed in 95% ethanol for 30 seconds. EA50 and Orange G were applied to half of the slides for 3 minutes and to the remaining slides for 6 minutes. All of the slides were then rinsed 2 times in 95% ethanol, 3 times in 100% ethanol, and 3 times in xylene for 30 seconds per rinse. The slides were then coverslipped with permanent mounting media and analyzed as described above in Examples 1 and 2.
Results
A panel of 5 NIL and 5 HSIL cases were each subjected to 3 minutes or 6 minutes of staining with EA50 and Orange G in the Pap staining method. Results indicated minimal difference between the 3 minute and the 6 minute staining protocols. The slides subjected to 3 minutes of Pap staining displayed slightly less intense staining. Furthermore, the ICC positive staining HSIL cells were readily observed with the Pap counterstain.
Example 7
Combined Immunocytochemistry and Pap Staining Procedure (Optimization of Pap Staining)
The combined immunocytochemistry and Pap staining procedure outlined in Example 6 was modified to optimize the Pap staining parameters in order to maximize the contrast between the chromogen (i.e., DAB) staining of the immunocytochemistry method and the level of Pap staining.
Slides were prepared, pretreated, and subjected to automated immunocytochemistry as described above in Example 6. The slides were then stained with a conventional Pap stain essentially as described in Example 6, with the following modifications. Hematoxylin was tested using the Harris formulation along with Myers formulation. EA/Orange G was applied for 3 minutes or 6 minutes. Additionally, there were 3 changes of 95% ethanol after the EA/Orange G addition.
Slides received a determination of positive, negative, or unsatisfactory based upon the immunocytochemistry staining. Additionally, slides were evaluated morphologically for comparison with the incoming Pap diagnosis.
Results







TABLE 39







Results of Combined Immunocytochemistry and Pap Staining Method









Incoming Pap
ICC



Diagnosis
Results
Comments





NIL
Negative
All cases confirmed as NIL.


n = 7


LSIL
Negative
5 of the 6 LSIL cases did not have LSIL


n = 6

cells on the slides. These cases were




either NIL or ASC-US.


HSIL
Positive
All cases confirmed as HSIL.


n = 6


Cancer
Positive
All cases were squamous cell carcinoma.


n = 4









The combined ICC and Pap staining procedure permitted both morphological analysis and assessment of biomarker overexpression. Additional experimentation will be required to further optimize the method.
Example 8
Immunocytochemistry Kit for the Detection of Biomarker Overexpression in Cervical Samples
I. Principles of the Procedure
An immunocytochenical test kit contains reagents required to complete a three-step immunocytochemical staining procedure for routinely prepared monolayer cervical specimens. Following incubation with the monoclonal antibody cocktail, this kit employs a ready-to-use visualization reagent based on dextran technology. This reagent consists of a secondary goat anti-mouse antibody molecule and horseradish peroxidase molecules linked to a dextran polymer backbone. The enzymatic conversion of the subsequently added chromogen results in the formation of a visible reaction product at the antigen(s) site. The specimen is then counterstained with hematoxylin, a bluing agent is applied, and the slide is coverslipped. Results are interpreted using a light microscope. A positive result indicative of cervical high-grade is achieved when cells of interest are stained brown.
A gallery of potentially positive cells may be created using automated imaging equipment. The gallery then can be reviewed to determine a positive result or negative result.
The immunocytochemical test kit is applicable for both manual and automated staining.
II. Reagents Provided
The following materials, sufficient for 75 monolayer preparations using 200 μL of the ready-to-use mouse monoclonal cocktail per preparation, were included in the immunocytochemical test kit:







TABLE 40







Immunocytochemistry Kit Components









Vial




No.
Quantity
Description





1a
1 × 15 mL
Peroxidase-Blocking Reagent: Buffered hydrogen




peroxide plus stabilizer and proprietary components


1b
1 × 15 mL
Protein Blocking Reagent: Purified casein plus




proprietary combination of proteins in modified PBS




with preservative and surfactant


2
1 × 15 mL
Mouse Anti-Human Antibody Cocktail: Ready-to-use




monoclonal antibody cocktail supplied in TRIS




buffered solution with Tween 20, pH 7.4. Contains




0.39 mg/mL MCM2 mAb clone 27C5.6 (1:800




dilution), 0.918 mg/mL MCM2 mAb clone




26H6.19 (1:10,000 dilution), 100 μg/mL




Topo2a mAb clone SWT3D1 (1:10,000




dilution), stabilizing proteins and anti-microbial agent.


3a
1 × 15 mL
Mouse Probe Reagent: Binds to mouse monoclonal




antibodies


3b
1 × 15 mL
Polymer Reagent: Polymer conjugated with




horseradish peroxidase that binds to Mouse Probe




Reagent


4a
1 × 18 mL
DAB Substrate Buffer: Substrate buffer used in the




preparation of the DAB Chromogen


4b
 1 × 1 mL
DAB Chromogen: 3,3′-diaminobenzidine chromogen




solution


5
1 × 18 mL
Hematoxylin Counterstain: aqueous based Mayers




Hematoxylin


6
1 × 18 mL
Bluing Agent: Tris buffered saline, pH 7.4 with Tween




20 and 0.09% NaN3









The following materials and reagents were required to perform the Immunocytochemistry methods but were not supplied in the kit:

    
    
        Absorbent Wipes
        SiHa Cell Line (TriPath Imaging,Inc.)
        Deionized or Distilled Water
        Ethanol (95% and 100)
        Glass Coverslips
        Gloves
        Humid Chamber
        Light Microscope (10×, 20×, 40× objectives)
        Mounting Media
        Pipettes and Pipette Tips (capable of delivering 20 μl, 200 μl and 1000 μl volumes)
        SureSlide Preparation Buffer (TriPath Imaging, Inc.)—Pretreatment Buffer (0.5% sodium laureth-13-carboxylate (Sandopan LS) in deionized H20)
        Staining Jars or Baths
        Timer (capable of 1-60 minute intervals)
        Tris Buffered Saline (TBS)
        Tween 20
        Universal Mouse IgG Negative Control
        Vortexer
        Xylene or Xylene Substitutes
        Steamer/waterbath

III. Instructions for Use

Specimen Preparation

    
    


The following steps were followed for the preparation of cervical samples:

    
    
        Consult the Operator's Manual for the SurePath PrepStain SystemTM for the preparation of slides from residual specimens.
        Add 8 mL of SurePathTM preservative fluid to the residual sample in the SurePathTM vial (approx. 2 mLs). The diluted sample is processed on the PrepMateTM using the standard technique and on the PrepStainTM using the GYN version 1.1, Slide Preparation.
        Prepared slides are immediately placed into the pretreatment buffer for a minimum of 1 hour with a maximum of 72 hours prior to immunostaining.
        Epitope retrieval must be used for optimal kit performance. This procedure involves soaking prepared slides in the pretreatment buffer for a minimum of 1 hour at room temperature followed by heating slides in the pretreatment buffer to 95° C. Slides are held at 95° C. for 15 minutes and allowed to cool down at room temperature for 20 minutes. The use of a calibrated waterbath or vegetable steamer capable of maintaining the required temperature is recommended. Laboratories located at higher elevations should determine the best method of maintaining the required temperature. The staining procedure is initiated immediately following epitope retrieval and cool down. Deviations from the described procedure may affect results.

Reagent Preparation

    
    


The following reagents were prepared prior to staining:
Tris Buffered Saline with 0.05% Tween 20 (TBST)


    
    
        Prepare TBS according to manufacturer's specifications.
        Add Tween 20 to a final concentration of 0.05%.
        Store at room temperature if used within one week.
        Unused solution may be stored at 2-8° C. for 3 months.
        Solution is clear and colorless. Discard diluted solution if cloudy in appearance.

Substrate-Chromogen Solution (DAB) (Volume Sufficient for 5 Slides)

        Transfer 1 mL of DAB Buffered Substrate to a test tube.
        Add one drop (20-30 uL) of DAB+ Chromogen. Mix thoroughly and apply to slides with a pipette.
        Prepare Substrate-Chromogen solution fresh daily.
        Any precipitate developing in the solution does not affect staining quality.

IV. Staining Protocol (Performed at Room Temperature, 20-25° C.)

    
    


The following steps were performed for immunostaining of the cervical cytology samples:
Staining Procedural Notes


    
    
        The user should read these instructions carefully and become familiar with all components prior to use.
        All reagents are equilibrated to room temperature (20-25° C.) prior to immunostaining. All incubations are performed at room temperature.
        Do not allow slides to dry out during the staining procedure. Dried cellular preparations may display increased non-specific staining. Cover slides exposed to drafts. Slides should be placed in a humid chamber for prolonged incubations.

Epitope Retrieval

        Place the prepared slides in the pretreatment buffer for a minimum of 1 hour to a maximum of 72 hours.
        Incubate for 15 minutes at 95° C.
        Remove the entire coplin jar with slides from the waterbath or steamer and allow slides to cool in the buffer for 20 minutes.
        Rinse the slides with diH2O and transfer to a TBST bath.

Peroxidase Blocking

        Tap off excess buffer.
        Load slides into prepared humidity chamber (filled with water moistened paper towels or gauze).
        Apply 200 μL Peroxidase Block reagent to cover the cell deposition area.
        Incubate 5 minutes (±1 minute).
        Rinse slides in TBST, 3 changes, 2 minutes each.

Protein Block

        Tap off excess buffer.
        Load the slides into the prepared humidity chamber (filled with water moistened paper towels or gauze).
        Apply 200 μL of Protein Block to completely cover cell deposition area.
        Incubate 5 minutes (±1 minute).
        Do not rinse slides.

Primary Antibody Cocktail

        Tap off excess Protein Block.
        Load the slides into the prepared humidity chamber (filled with water moistened paper towels or gauze).
        Apply 200 μL primary antibody cocktail (to completely cover cell deposition area.
        Incubate 30 minutes at room temperature.
        Rinse each slide individually with TBST using a wash bottle (do not focus the flow directly on the cell deposition area). Load slides into a slide rack.
        Rinse slides in TBST, 3 changes, 2 minutes each.

Detection Chemistry

        Tap off excess buffer.
        Load slides into prepared humidity chamber (filled with water moistened paper towels or gauze).
        Apply 200 μL Mouse Probe to completely cover cell deposition area.
        Incubate 20 minutes (±1 minute).
        Rinse slides in TBST, 3 changes, 2 minutes each.
        Tap off excess buffer.
        Load slides into prepared humidity chamber (filled with water moistened paper towels or gauze).
        Apply 200 μL of Polymer to cover cell deposition area.
        Incubate for 20 minutes (±1 minute).
        Rinse slides in TBST bath, 3 changes, 2 minutes each.
        Tap off excess buffer.
        Load the slides into the prepared humidity chamber (filled with water moistened paper towels or gauze).
        Apply 200 μL of DAB working solution to completely cover cell deposition area.
        Incubate for 5 minutes (±1 minute).
        Rinse slides for 5 minutes in diH2O for 5 minutes.

Counterstain

        Rinse slides in TBST, 1 change for 2 minutes.
        Load slides into prepared humidity chamber (filled with water moistened paper towels or gauze).
        Apply 200 μL of hematoxylin to completely cover cell deposition area.
        Incubate for 1 minute (±10 seconds).
        Rinse slides for 3 minutes in running H2O.
        Load slides into prepared humidity chamber (filled with water moistened paper towels or gauze).
        Blue slides by applying 200 μL Bluing Agent for 1 minute (±10 seconds).
        Repeat running water rinse for 1 minute.

Mounting

        Immerse slides in 95% ethanol, 1 minute or 25 dips.
        Immerse slides in absolute alcohol, 4 changes, 1 minute each or 25 dips.
        Clear with xylene, 3 changes, 1 minute each or 25 dips.
        Coverslip slides with non-aqueous, permanent mounting media using glass coverslips.

V. Quality Control

    
    


The following quality control issues were considered when using the immunocytochemistry kit described in this example:
Variability in results is often derived from differences in specimen handling and changes in test procedures. Consult the proposed quality control guidelines of the NCCLS Quality Assurance for Immunocytochemistry for additional information.
Control Cell Line is available from TriPath Imaging, Inc. Each vial contains a cervical cancer cell line, which is processed in a similar manner as the clinical specimens. Two slides should be stained in each staining procedure. The evaluation of the control slide cell line indicates the validity of the staining run.
VI. Interpretation of Staining
Control Slides:
The control slide stained with the immunocytochemical test kit were examined first to ascertain that all reagents functioned properly. The presence of a brown (3,3′-diaminobenzidine tetrahydrochloride, DAB) reaction product in the nuclei of the cells were indicative of positive reactivity.
Patient Specimens:
Slide evaluation was performed by a cytotechnologist or pathologist using a light microscope. Cells were reviewed manually or electronically stored in an image gallery derived from a light microscope.
Approximately 1610 cervical samples representing various diagnoses were collected. The following table indicates the number of samples analyzed using the immunocytochemistry kit within each diagnosis group, as determined by conventional Pap staining or biopsy.







TABLE 41







Patient Specimens within Each Diagnosis Group (Pap Staining)











Cytology





Results
Number
%















NIL
671
41.7%



LSIL
395
24.53% 



ASCUS
349
21.68% 



HSIL
150
9.32%



ASC-H
38
2.36%



AGUS
6
0.37%



SCC
1
0.06%



Total
1610

















TABLE 42







Patient Specimens within Each Diagnosis Group (Biopsy)











Biopsy





Results
Number
%















NIL
968
60.20%



CIN1
369
22.95%



CIN2
140
8.71%



CIN3
131
8.15%



Missing
2



Total
1610










Slide Scoring Guide

The following procedure was followed for the scoring of all slides analyzed by the immunocytochemistry methods described in this example:
Step 1: Is it an Adequate Specimen?
The Bethesda System for Reporting Cervical Cytology (second edition) states, “An adequate liquid-based preparation should have an estimated minimum of at least 5000 well-visualized/well-preserved squamous cells.” These same criteria were applied when evaluating all of the slides. However, as with a routine Pap preparation, any specimen with abnormal cells, which are exhibiting a positive molecular reaction, was, by definition, satisfactory for evaluation. If the answer to this step was “yes”, the cytotechnologist proceeded to the next step; if the answer was “no,” the result was Unsatisfactory for Evaluation.
Step 2: Is there Moderate to Intense Brown Nuclear Staining in Epithelial Cells?
The detection chemicals used in the immunocytochemistry kit of this example (e.g., SureDetect Detection Chemistry Kit) stains dysplastic nuclei associated with ≧CIN 2 with a brown chromagen, DAB. To answer “yes” to this step, samples were analyzed for brown staining that was easily visualized. If just a faint amount, or “blush,” of brown was seen, this was not enough to warrant a rendering of positive. If no brown nuclear stain was seen, this was deemed a negative test result. If there was adequate brown stain, the analysis proceeded to the next step.
Step 3: Is this a Squamous (or Glandular) Cell with Brown Nuclear Staining and is the Cell≧ASC (AGC)?
Using the same morphological criteria outlined in The Bethesda System for Reporting Cervical Cytology (2nd Ed.) (“TBS”), it was determined if the squamous cell containing the brown nucleus was ≧ASC (atypical squamous cells). This would include ASC-US, ASC-H, LSIL, HSIL, and cancer. If the cell was glandular in appearance, the TBS criteria for determining if a cell is ≧AGC (atypical glandular cells) applied. This would include endocervical AGC, endometrial AGC, AIS, and adenocarcinoma. If the cell was considered to be ≧ASC (or ≧AGC) than this would result in a positive test result. If the cells in question were consistent with NILM (negative for intraepithelial lesion or malignancy) this would be a negative test result.
VII. Results
27 cases that were originally classified as NIL by conventional Pap staining methods stained positive in the immunocytochemistry test. Of these 27 cases, 7 were classified as HSIL, 10 as ASC-H, 3 as ASC-US, and 3 as indeterminate upon review by aboard certified pathologist. The 7 HSIL cases are considered high-grade cervical disease. These 27 cases were identified by positive immunostaining in the immocytochemistry assay, thereby indicating the value of the methods disclosed herein for identifying patients misclassified as NIL by Pap staining.
Biopsy results were not obtained for all NIL specimens. Estimates of sensitivity and positive predictive value (PPV) for the immunocytochemistry method described in this example were calculated based on comparison with the “gold standard” biopsy results. Single biopsy has limitations as a gold standard. PPV for the ICC assay will improve by serial monitoring of the patient or utilizing a more aggressive surgical endpoint such as loop electrosurgical excision procedure or cone biopsy. Single biopsy is known to have a false negative result for disease of at least 31%. See Elit et al. (2004) J. Lower Genital Tract Disease 8(3):181-187.







TABLE 43







Estimated sensitivity and positive predictive


value of ICC test based on the biopsy results













ASC-H
ASCUS
LSIL
HSIL
≧ASCUS
















Sensitivity
76.5%
92.6%
97.7%
98.5%
96.2%



(52.7%,
(76.6%,
(92.1%,
(94.6%,
(93.1%,



90.4%)*
97.9%)
99.4%)
99.6%)
97.9%)


PPV
59.1%
26.0%
31.0%
90.1%
46.9%



(38.7%,
(18.3%,
(25.9%,
(84.1%,
(42.8%,



76.7%)
35.6%)
36.7%)
94.0%)
51.2%)





*(95% confidence interval)






The sensitivity and PPV of the immunocytochemistry method was also compared to those obtained with conventional Pap staining. Two clinical endpoints for Pap staining (i.e., ≧LSIL and ≧HSIL) were used. Again, the standard for all calculations was the biopsy result.







TABLE 44







Comparison of Pap Test and Immunocytochemistry Method











≧LSIL
≧HSIL




(with Pap test)
(with Pap test)
≧ASCUS (with ICC)














Sensitivity
76.5%
92.6%
97.7%



(52.7%, 90.4%)*
(76.6%, 97.9%)
(92.1%, 99.4%)


PPV
59.1%
26.0%
31.0%



(38.7%, 76.7%) 
(18.3%, 35.6%)
(25.9%, 36.7%)





*(95% confidence interval)






The results presented in Table 42 indicate that the immunocytochemistry method detected more high-grade cervical disease samples, while maintaining a high PPV.
There were 14 false negatives in this study using the immunocytochemistry kit. HPV testing was conducted on 13 of the 14 patient samples. No remaining sample was available for one of the false negative patients.
Genomic DNA was isolated from the cervical cytology samples using the NucleoSpin® Tissue DNA Kit (BD Clontech, Cat#635967). For quality control purposes, PCR analysis of beta-globin, a housekeeping gene, was performed.
HPV L1 gene amplification was performed as described in the art by both conventional L1 PCR with MY09/11 primer set and by nested PCR with MY09/11 and GP5+/6+ primer sets to improve detection sensitivity. DNA sequencing of the L1 amplicon was further performed to identify the type(s) of HPV(s) present.
Good quality genomic DNA was isolated from 10 out of the 13 clinical cytology samples. 3 samples had poor quality genomic DNA as indicated by beta-globin PCR analysis. HPV DNA was either undetectable or negative in 10 of the 13 samples using both conventional L1 PCR (with MY09/11 primers) and nested L1 PCR (with MY09/11 and GP5+/6+ primers). This data indicates that a sampling error occurred for a majority of the false negative samples, given that HPV is positive for high-grade cervical disease (sensitivity of >92%).
Example 9
MCM6 Antibody Selection
Polydoma Screening
Polydomas provided in multi-well tissue culture plates were screened to identify MCM 6 biomarker-specific antibodies that possess the desired traits of sensitivity and specificity. A tissue microarray comprising multiple normal (i.e., no CIN), CINIII, squamous cell carcinoma, and adenocarcinoma samples on a single slide was generated. Undiluted supernatants from each well containing a polydoma were assayed for positive staining of the tissue microarray. Background, i.e. non-specific binding, was essentially ignored at this stage. Eleven of the 35 polydomas tested produced positive staining results and were selected for further analysis.
In order to determine the specificity of the selected polydomas, the staining patterns obtained with the polydoma supernatants were compared with those obtained with a commercially available MCM 6 antibody (BD Transduction Laboratories). The staining patterns obtained with the polydoma supernatants appeared to be more specific than those observed with the commercial MCM 6 antibody (FIG. 17).
The 11 selected polydomas were then subjected to a limiting dilution process. Thirty limiting dilutions, resulting from the supernatants of the selected polydomas, were assayed for positive staining of a tissue microarray comprising multiple normal (i.e., no CIN), CINIII, squamous cell carcinoma, and adenocarcinoma samples. Two limiting dilution clones, 9D4.3 and 9D4.4, were selected as the best supernatants based on positive staining of abnormal and cancerous cervical tissue samples. Varying dilutions of these clones were then tested for their reactivity to NIL, LSIL, HSIL tissue and pooled liquid based cytology samples. Clone 9D4.3 at a 1:100 dilution produced the maximal signal to noise ratio and was selected for further characterization.
Characterization of MCM 6, Clone 9D4.3
In order to further characterize clone 9D4.3, the clone was assayed for positive staining of 40 liquid based cytology samples selected from the following diagnostic categories: NIL (7), LSIL (10), HSIL (18), and cervical carcinoma (5). Slides were prepared using the PrepStainTM slide processor (TriPath Imaging, Inc.) for each of the 40 samples. Two slides per sample were each stained with an MCM 2 antibody (Dako) and clone 9D4.3. The remaining slides were used for PAP staining or as a negative control.
To prepare slides, each sample was centrifuged for 2 minutes at 200× g to form a pellet, and the supernatant was decanted. 2 mL of deionized water was added to each sample, and the samples were vortexed and then centrifuged for 5 minutes at 600× g. After decanting the supernatant, an additional 700 μL of tris buffered water was added. Finally the samples were loaded onto the PrepStainTM slide processor (Tripath Imaging, Inc.), version 1.1, and the Transfer Only program was run.
All slides were held in 95% ETOH for at least 24 hours and no more than 3 days after preparation. Antigen retrieval for MCM2 was achieved by placing the slides in a 1× Target Retrieval Solution pH 6.0 (DAKO S1699)/dH20 bath, preheated to 95° C., for 25 minutes in a steamer. For MCM6, antigen accessibility was achieved by placing the slides in a 1× Tris pH 9.5 buffer (Biocare)/dH20 bath, preheated to 95° C., for 25 minutes in a steamer. After steaming, all slides were allowed to cool at room temperature for 20 minutes.
Slides were stained by immunocytochemistry using the DAKO Universal Autostainer as described in Example 1, “Automated Immunocytochemistry.” The slides were screened and evaluated by an experienced cytotechnologist for a morphological determination of diagnostic category. The samples were assessed for marker staining intensity (0-3), percentage of positive-staining cells, and the location of the marker staining (nuclear, cytoplasmic, membrane, or a combination). Intensity of cell staining was given a score of 0-3. Cells scoring ≧1.5 were counted. Mature normal-appearing squamous cells and normal-appearing glandular cells were not counted as positive when staining brown. However, squamous metaplastic cells were counted as positive along with abnormal cells. The immunocytochemistry slides were then given a designation of TN (true negative), FN (false negative), TP (true positive), or FP (false positive).







TABLE 45







Clone 9D4.3 (MCM6)














TP
FP
FN
TN
Indet.
Total



















NIL
0
0
0
1
0
1



LSIL
0
1
0
9
0
10



HSIL
23
0
1
0
0
24



Cancer
5
0
0
0
0
5




28
1
1
10
0
40







Sensitivity 0.9655



Specificity 0.9091



PPP 0.9655



NPP 0.9091













TABLE 46







MCM2














TP
FP
FN
TN
Indet.
Total



















NIL
0
0
0
1
0
1



LSIL
0
1
0
9
0
10



HSIL
23
0
1
0
0
24



Cancer
4
0
1
0
0
5




27
1
2
10
0
40







Sensitivity 0.9310



Specificity 0.9091



PPP 0.9643



NPP 0.8333



Calculations Used



Sensitivity = TP/(TP + FN)



Specificity = TN/(FP + TN)



Positive Predictive Power (PPP) = TP/(TP + FP)



Negative Predictive Power (NPP) = TN/(FN + TN)






The sensitivity and specificity for clone 9D4.3 was comparable to that obtained with the commercially available MCM2 antibody. One NIL case was negative for both antibodies. 9 of 10 LSIL cases were negative with clone 9D4.3 and the commercial MCM2 antibody. 23 of 24 HSIL cases were positive with clone 9D4.3 and the commercial MCM2 antibody. With the cervical cancer samples, 5 of 5 were positive with clone 9D4.3, and 4 of 5 were positive with the MCM 2 antibody.
Purification of MCM 6, Clone 9D4.3
Because of its sensitivity, specificity, and the presentation of a nuclear staining pattern, clone 9D4.3 was purified for further analysis. Purified antibody was obtained using Streamline rProteinA (Amersham Biosciences) affinity adsorption chromatography, in accordance with standard methods. The resulting antibody solution was then tested for reactivity against HSIL liquid-based cervical cytology pools at various dilutions between 1:500 and 1:6000. Signal was evident out to a titer of 1:6000.
Example 10
Real-Time PCR Detection of Biomarkers in Clinical Tissue Samples
TaqMan® real-time PCR was performed with the ABI Prism 7700 Sequence Detection System (Applied Biosystems). The primers and probes were designed with the aid of the Primer ExpressTM program, version 1.5 (Applied Biosystems), for specific amplification of the targeted cervical biomarkers (i.e., MCM7, p21waf1, p14ARF/p16, cyclin E1, and cyclin E2) in this study. The sequence information for primers and probes is shown below:








MCM7:



Primer Name: MCM7_T1T3-F








(SEQ ID NO:25)









Sequence: CTCTGAGCCCGCCAAGC



 


Primer Name: MCM7_T1T3-R








(SEQ ID NO:26)









Sequence: TGTAAGAACTTCTTAACCTTTTCCTTCTCTA



 


Probe Name: MCM7_T1T3-Probe








(SEQ ID NO:27)









Sequence: CCCTCGGCAGCGATGGCACT



 


Primer Name: MCM7_T2T4-F








(SEQ ID NO:28)









Sequence: GAGGAATCCCGAGCTGTGAA



 


Primer Name: MCM7_T2T4-R








(SEQ ID NO:29)









Sequence: CCCGCTCCCGCCAT



 


Probe Name: MCM7_T2T4-Probe








(SEQ ID NO:30)









Sequence: CCCATGTGCTTCTTTGTTTACTAAGAGCGGAA



 


Primer Name: MCM7_T2-F








(SEQ ID NO:31)









Sequence: GTCCGAAGCCCCCAGAA



 


Primer Name: MCM7_T2-R








(SEQ ID NO:32)









Sequence: CCCGACAGAGACCACTCACA



 


Probe Name: MCM7_T2-Probe








(SEQ ID NO:33)









Sequence: CAGTACCCTGCTGAACTCATGCGCA



 


Primer Name: MCM7_T3T4-F








(SEQ ID NO:34)









Sequence: CGCTACGCGAAGCTCTTTG



 


Primer Name: MCM7_T3T4-R








(SEQ ID NO:35)









Sequence: CCTTTGTTTGCCATTGTTCTCTAA



 


Probe Name: MCM7_T3T4-Probe








(SEQ ID NO:36)









Sequence: TGCCGTACAAGAGCTGCTGCCTCA



 


p21waf1:


Primer Name: p21T1T2-F








(SEQ ID NO:37)









Sequence: CAAACGCCGGCTGATCTT



 


Primer Name: p21T1T2-R








(SEQ ID NO:38)









Sequence: CCAGGACTGCAGGCTTCCT



 


Probe Name: p21T1T2-Probe








(SEQ ID NO:39)









Sequence: CAAGAGGAAGCCCTAATCCGCCCA



 


Primer Name: p21T2-F








(SEQ ID NO:40)









Sequence: GAGCGGCGGCAGACAA



 


Primer Name: p21T2-R








(SEQ ID NO:41)









Sequence: CCGCGAACACGCATCCT



 


Probe Name: p21T2-Probe








(SEQ ID NO:42)









Sequence: CCCAGAGCCGAGCCAAGCGTG



 


Primer Name: p21T3-F








(SEQ ID NO:43)









Sequence: TGGAGACTCTCAGGGTCGAAA



 


Primer Name: p21T3-R








(SEQ ID NO:44)









Sequence: TCCAGTCTGGCCAACAGAGTT



 


Probe Name: p21T3-Probe








(SEQ ID NO:45)









Sequence: CGGCGGCAGACCAGCATGAC



 


p14ARF/p16:


Primer Name: p16T4-F








(SEQ ID NO:46)









Sequence: GCC CTC GTG CTG ATG CTA CT



 


Primer Name: p16T4-R








(SEQ ID NO:47)









Sequence: TCA TCA TGA CCT GGT CTT CTA GGA



 


Probe Name: p16T4-Probe








(SEQ ID NO:48)









Sequence: AGC GTC TAG GGC AGC AGC CGC



 


Primer Name: p16T1-F








(SEQ ID NO:49)









Sequence: TGCCCAACGCACCGA



 


Primer Name: p16T1-R








(SEQ ID NO:50)









Sequence: GGGCGCTGCCCATCA



 


Probe Name: p16T1-Probe








(SEQ ID NO:51)









Sequence: TCGGAGGCCGATCCAGGTCATG



 


Primer Name: p16T2-F








(SEQ ID NO:52)









Sequence: AAGCTTCCTTTCCGTCATGC



 


Primer Name: p16T2-R








(SEQ ID NO:53)









Sequence: CATGACCTGCCAGAGAGAACAG



 


Probe Name: p16T2-Probe








(SEQ ID NO:54)









Sequence: CCCCCACCCTGGCTCTGACCA



 


Primer Name: p16T3-F








(SEQ ID NO:55)









Sequence: GGAAACCAAGGAAGAGGAATGAG



 


Primer Name: p16T3-R








(SEQ ID NO:56)









Sequence: TGTTCCCCCCTTCAGATCTTCT



 


Probe Name: p16T3-Probe








(SEQ ID NO:57)









Sequence: ACGCGCGTACAGATCTCTCGAATGCT



 


Primer Name: p16Universal-F








(SEQ ID NO:58)









Sequence: CACGCCCTAAGCGCACAT



 


Primer Name: p16 Universal-R








(SEQ ID NO:59)









Sequence: CCTAGTTCACAAAATGCTTGTCATG



 


Probe Name: p16 Universal-Probe








(SEQ ID NO:60)









Sequence: TTTCTTGCGAGCCTCGCAGCCTC



 


Cyclin E1:


Primer Name: CCNE1T1T2-F








(SEQ ID NO:61)









Sequence: AAAGAAGATGATGACCGGGTTTAC



 


Primer Name: CCNE1T1T2-R








(SEQ ID NO:62)









Sequence: GAGCCTCTGGATGGTGCAA



 


Probe Name: CCNE1T1T2-P








(SEQ ID NO:63)









Sequence: CAAACTCAACGTGCAAGCCTCGGA



 


Primer Name: CCNE1T1-F








(SEQ ID NO:64)









Sequence: TCCGCCGCGGACAA



 


Primer Name: CCNE1T1-R








(SEQ ID NO:65)









Sequence: CATGGTGTCCCGCTCCTT



 


Probe Name: CCNE1T1-Probe








(SEQ ID NO:66)









Sequence: ACCCTGGCCTCAGGCCGGAG



 


Cyclin E2


Primer Name: CCNE2T1T2-F








(SEQ ID NO:67)









Sequence: GGAATTGTTGGCCACCTGTATT



 


Primer Name: CCNE2T1T2-R








(SEQ ID NO:68)









Sequence: CTGGAGAAATCACTTGTTCCTATTTCT



 


TaqMan Probe Name: CCNE2TLT2-P








(SEQ ID NO:69)









Sequence: CAGTCCTTGCATTATCATTGAAACACCTCACA



 


Primer Name: CCNE2T1T3-F








(SEQ ID NO:70)









Sequence: TCAACTCATTGGAATTACCTCATTATTC



 


Primer Name: CCNE2T1T3-R








(SEQ ID NO:71)









Sequence: ACCATCAGTGACGTAAGCAAACTC



 


TaqMan Probe Name: CCNE2T1T3-P








(SEQ ID NO:72)









Sequence: CCAAACTTGAGGAAATCTATGCTCCTAAACTCCA



 


Primer Name: CCNE2T2-F








(SEQ ID NO:73)









Sequence: TTTTGAAGTTCTGCATTCTGACTTG



 


Primer Name: CCNE2T2-R








(SEQ ID NO:74)









Sequence: ACCATCAGTGACGTAAGCAAGATAA



 


TaqMan Probe Name: CCNE2T2-P








(SEQ ID NO:75)









Sequence: AACCACAGATGAGGTCCATACTTCTAGACTGGCT







The probes were labeled with a fluorescent dye FAM (6-carboxyfluorescein) on the 5′ base, and a quenching dye TAMRA (6-carboxytetramethylrhodamine) on the 3′ base. The sizes of the amplicons were around 100 bp. 18S Ribosomal RNA was utilized as an endogenous control. An 18S rRNA probe was labeled with a fluorescent dye VICTM. Pre-developed 18S rRNA primer/probe mixture was purchased from Applied Biosystems. 5 μg of total RNA extracted from normal (N) or cancerous (T) cervical tissues was quantitatively converted to the single-stranded cDNA form with random hexamers by using the High-Capacity cDNA Archive Kit (Applied Biosystems). The following reaction reagents were prepared:










20X Master Mix of Primers/Probe (in 200 μl)


















180 μM Forward primer
20 μl



180 μM Reverse primer
20 μl



100 μM TaqMan probe
10 μl



H2O
150 μl 




















Final Reaction Mix (25 μl/well)
















20X master mix of primers/probe
1.25 μl


2X TaqMan Universal PCR master mix (P/N: 4304437)
12.5 μl


cDNA template
 5.0 μl


H2O
6.25 μl









20× TaqMan Universal PCR Master Mix was purchased from Applied Biosystems. The final primer and probe concentrations, in a total volume of 25 μl, were 0.9 μM and 0.25 μM, respectively. 10 ng of total RNA was applied to each well. The amplification conditions were 2 minutes at 50° C., 10 minutes at 95° C., and a two-step cycle of 95° C. for 15 seconds and 60° C. for 60 seconds for a total of 40 cycles. At least three no-template control reaction mixtures were included in each run. All experiments were performed in triplicate.
At the end of each reaction, the recorded fluorescence intensity is used for the following calculations: Rn+ is the Rn value of a reaction containing all components. Rn− is the Rn value of an unreacted sample (baseline value or the value detected in NTC). ΔRn is the difference between Rn+ and Rn− and is an indicator of the magnitude of the signal generated by the PCR. The comparative CT method, which uses no known amount of standard but compares the relative amount of the target sequence to any reference value chosen (e.g., 18S rRNA), was used in this study. The TaqMan® Human Endogenous Control Plate protocol was used to convert raw data for real-time PCR data analysis.
Results
The results obtained with each biomarker and with the specific primers are listed below in tabular form. Results obtained with normal cervical tissue samples (i.e., NIL) are designated N; those obtained with cervical cancer tissues are labeled T.







TABLE 47







MCM7 TaqMan ® Results














Sample
T2
T5
T1T3
T2T4
T3T4


















CV01-T
4
0.04
29.9
4.5
1.4



CV03-T
5.7
0.02
36.8
6.1
2.6



CV05-T
4.13
0.08
17.3
1.35
3.68



CV07-T
2.6
0.06
18.77
0.88
3.27



CV09-T
4.96
0.08
15.01
3.69
3.22



CV11-T
5.9
0.01
7.37
3.08
1.75



CV13-T
6.74
0.04
19.74
4.55
4.11



CV15-T
3.04
0.05
3.65
3.43
1.25



CV17-T
5.21
0.02
20.07
2.74
1.56



CV19-T
3.34
0.09
21.17
2.88
6



CV21-T
6.7
0.08
10.64
4.75
4.59



CV23-T
7.08
0.33
32.17
5.6
4.25



CV25-T
4.87
0.03
18.11
4.58
4.51



CV27-T
4.24
0.03
36.25
4.6
2.82



MEAN
4.89
0.07
20.50
3.77
3.22



MEDIAN
4.89
0.05
19.74
3.77
3.22



STD
1.32
0.07
9.46
1.39
1.32



CV02-N
2.5
0.02
10.6
2.6
1.1



CV04-N
4.6
0.02
7.1
4.8
2.4



CV06-N
1.75
0.01
2.14
1.36
2.63



CV08-N
1.35
0.01
4.8
1.71
1.54



CV10-N
5.6
0.03
5.07
5.12
1.85



CV12-N
5.68
0.02
7.34
3.19
2.29



CV16-N
4.35
0.08
3.72
2.75
1.78



CV18-N
3.98
0.01
4.74
3.63
1.7



CV20-N
2.03
0.03
5.42
1.4
2.78



CV22-N
2.66
0.02
4.33
2.26
2.42



CV24-N
4.88
0.09
9.03
1.53
2.77



CV28-N
2.71
0.01
10.38
1.36
1.7



MEAN
3.51
0.03
6.22
2.64
2.08



MEDIAN
3.51
0.02
5.42
2.60
2.08



STD
1.40
0.03
2.48
1.21
0.50

















TABLE 48







p21waf1TaqMan ® Results












Patients
T1T2
T2
T3
















Pt01-T
23.33
0.06
0.00



Pt02-T
14.66
0.01
0.00



Pt03-T
11.86
0.00
0.00



Pt04-T
27.04
0.01
0.00



Pt05-T
14.72
0.00
0.00



Pt06-T
22.84
0.01
0.00



Pt07-T
14.04
0.00
0.00



Pt08-T
31.93
0.01
0.01



Pt09-T
35.02
0.00
0.00



Pt10-T
13.2
0.00
0.00



Pt11-T
24.87
0.01
0.00



Pt12-T
10.85
0.00
0.00



Pt13-T
36.51
0.02
0.01



Pt14-T
12.72
0.00
0.00



Pt15-T
10.64
0.00
0.00



Pt16-T
22.58
0.04
0.00



Pt17-T
39.64
0.14
0.04



Pt01-N
4.57
0.03
0.00



Pt02-N
5.57
0.00
0.00



Pt03-N
3.54
0.00
0.00



Pt04-N
8.18
0.00
0.00



Pt05-N
5.4
0.10
0.00



Pt06-N
11.01
0.00
0.00



Pt08-N
10.39
0.00
0.00



Pt09-N
9.11
0.00
0.00



Pt10-N
4.41
0.00
0.00



Pt11-N
8.64
0.00
0.00



Pt12-N
3.03
0.00
0.00



Pt14-N
3.55
0.00
0.00



Pt15-N
2.42
0.01
0.00



Pt17-N
11.46
0.05
0.01



T-mean
21.5559



N-mean
6.52



St. T-test =
7.3E−06

















TABLE 49







p14ARF/p16 TaqMan ® Results














Patient
T1
T2
T3
T4
UNIVERSAL


















Pt01-T
0.2
0.1
0.2
0.2
0.2



P102-T
16.3
11.2
5.1
21.7
36.5



Pt03-T
16.5
6.2
3.1
15.1
29.6



Pt04-T
10.1
2.8
2.6
13.2
27.7



Pt05-T
12.7
3.6
2.1
11.3
23.1



Pt01-N
0.1
0.1
0.1
0.1
0.1



P102-N
2.5
2.6
1.6
2.7
6.8



Pt04-N
2.6
0.6
0.8
2.4
5.8



Pt05-N
2.1
0.8
0.7
4.1
4.6



T-Mean
11.2
4.8
2.6
12.3
23.4



N-Mean
1.8
1.0
0.8
2.3
4.3

















TABLE 50







Cyclin E1 TaqMan ® Results















Patient
T1T2 Cancer M.
Cancer SD
T1T2 Normal M.
Normal SD
T1 Cancer M.
Cancer SD
T1 Normal M.
Normal SD


















Pt 01
12.19
0.12
4.11
0.13
1.34
0.04
0.5
0.03


Pt 02
16.72
0.21
4.44
0.34
1.35
0.02
0.47
0.05


Pt 03
11.45
0.41
2.81
0.13
1.17
0.01
0.06
0.02


Pt 04
21.33
0.45
5.33
0.09
0.76
0.1
0.23
0.01


Pt 05
11.17
0.25
3.68
0.15
0.95
0.05
0.15
0.03


Pt 06
21.65
0.24
3.11
0.22
0.89
0.03
0.13
0.02


Pt 07
23.26
0.54
0
0
0.75
0.06
0
0.01


Pt 08
8.37
0.24
3.1
0.01
0.12
0.01
0.13
0.02


Pt 09
17.74
0.43
2.17
0.08
0.73
0.02
0.09
0.01


Pt 10
18.51
0.29
4.56
0.17
1.37
0.03
0.41
0.04


Pt 11
10.58
0.52
3.92
0.12
0.57
0.01
0.23
0.03


Pt 12
33.67
0.58
7.87
0.1
0.78
0.01
0.28
0.05


Pt 13
36.9
0.41
0
0
1.05
0.04
0
0


Pt 14
31.01
0.29
6.01
0.26
1.68
0.05
0.24
0.03


Pt 15
7.35
0.23
1.24
0.09
0.34
0.08
0.08
0.02


Pt 16
12.71
0.61
3.72
0
1.1
0.06
0.07
0.01


Pt 17
12.13
0.21
11.46
0.15
0.34
0.07
0.05
0.01


Pt 18
14.22
0.14
5.94
0.06
0.73
0.08
0.26
0.04


Pt 19
12.69
0.81
3.52
0.02
0.41
0.04
0.24
0.02


Pt 20
16.56
0.16
6.1
0.12
0.17
0.02
0.06
0


Pt 21
11.63
0.23
3.01
0.06
0.54
0.04
0.23
0.01


Pt 22
17.39
0.34
2.36
0.02
0.47
0.02
0.24
0.05


Pt 23
16.56
0.16
2.1
0.02
0.18
0.03
0.09
0.01


Pt 24
22.23
0.33
4.06
0.28
1.9
0.17
0.52
0.01


Pt 25
13.98
0.48
3.72
0.05
0.54
0.04
0.23
0.01


Pt 26
22.71
0.76
4.48
0.07
0.47
0.02
0.24
0.05


Pt 27
16.17
0.4
5.64
0.3
0.18
0
0.12
0.01


Pt 28
12.6
0.56
3.8
0.06
0.29
0.03
0.05
0


Pt 29
13.69
0.34
3.1
0.18
0.29
0.03
0.11
0


Pt 30
17.69
0.61
4.3
0.11
0.36
0.01
0.03
0


Pt 31
20.46
0.3
3.91
0.21
0.47
0.03
0.08
0


Pt 32
18.38
0.18
3.16
0.06
0.42
0.02
0.17
0.01


Pt 33
21.1
0.62
4.52
0.33
1.07
0.05
0.24
0.01


Pt 34
21.5
1.37
4.56
0.13
0.24
0.01
0.11
0.01


Average
17.54

4.26

0.68

0.20


T/N
4.1


t-test P=
7.80E−14
















TABLE 51







Cyclin E2 TaqMan ® Results















T1T2

T1T3

T2




Std.

Std.

Std.


Patients
T1T2
Dev.
T1T3
Dev.
T2
Dev.
















Pt01-T
13.17
1.02
16.11
0.39
0.01
0.00


Pt02-T
13.42
0.3
18.12
2.21
0.15
0.02


Pt03-T
13.64
0.50
17.40
2.16
0.05
0.01


Pt04-T
19.37
1.41
24.26
1.01
0.01
0.00


Pt05-T
10.59
1.1
14.71
1.58
0.17
0.02


Pt06-T
7.96
0.91
9.32
0.51
0.06
0.01


Pt07-T
14.1
1.73
16.92
0.84
0.54
0.06


Pt08-T
8.11
0.67
9.50
0.66
0.34
0.07


Pt09-T
13.04
0.72
18.27
0.99
0.02
0.00


Pt10-T
19.56
2.29
23.42
0.00
0.02
0.01


Pt11-T
16.8
1.57
18.71
2.15
0.08
0.01


Pt12-T
16.05
0.85
18.81
0.74
0.91
0.01


Pt13-T
14.91
0.87
18.51
1.59
0.61
0.16


Pt14-T
14.89
0.32
20.49
0.86
0.42
0.03


Pt15-T
12.44
0.47
15.26
1.00
0.68
0.18


Pt16-T
11.54
1.58
13.13
0.75
1.02
0.14


Pt17-T
6.78
0.47
7.91
0.45
0.85
0.10


Pt01-N
4.89
0.21
5.94
0.53
0.00
0.00


Pt02-N
6.32
0.47
8.91
0.61
0.13
0.00


Pt03-N
4.8
0.31
5.89
0.30
0.04
0.00


Pt04-N
13.28
0.74
15.28
1.37
0.01
0.00


Pt05-N
6.51
1.2
9.04
0.82
0.16
0.02


Pt06-N
4.96
0.83
6.41
0.84
0.05
0.01


Pt08-N
6.48
0.73
6.82
0.60
0.07
0.02


Pt09-N
3.74
0.48
4.63
0.66
0.03
0.01


Pt10-N
10.32
0.93
11.31
0.89
0.02
0.00


Pt11-N
10.34
0.26
13.90
0.53
0.04
0.04


Pt12-N
13.81
1.69
16.60
1.45
0.24
0.07


Pt14-N
6.92
0.63
9.07
0.95
0.14
0.03


Pt15-N
4.8
0.73
8.55
1.40
0.10
0.03


Pt17-N
5.33
0.2
5.78
0.27
0.23
0.07


T-mean
13.32

16.52

0.35


N-mean
7.32

9.15

0.09


St. T-test
4.16E−05

3.31742E−05

0.008813









Example 11
Real-Time PCR Detection of Biomarkers in Clinical Tissue Samples
TaqMan® real-time PCR was performed as described in Example 9 using cervical cancer tissue samples (e.g., adenocarcinoma, squamous cell carcinoma) and normal cervical tissue samples. The primers and probes were designed with the aid of the Primer ExpressTM program, version 1.5 (Applied Biosystems), for specific amplification of the targeted cervical biomarkers (i.e., MCM2, MCM6, MCM7, and Topo2A) in this study. The sequence information for primers and probes is shown below:








TaqMan Primers



MCM2:


Primer Name: MCM2-F








(SEQ ID NO:80)









Sequence: 5′-GGAGGTGGTACTGGCCATGTA-3′



 


Primer Name: MCM2-R








(SEQ ID NO:81)









Sequence: 5′-GGGAGATGCGGACATGGAT-3′



 


TaqMan Probe Name: MCM2-P








(SEQ ID NO:82)









Sequence: 5′-CCAAGTACGACCGCATCACCAACCA-3′



 


MCM6:


Primer Name: MCM6-F








(SEQ ID NO:83)









Sequence: 5′-CATTCCAAGACCTGCCTACCA-3′



 


Primer Name: MCM6-R








(SEQ ID NO:84)









Sequence: 5′-ATGCGAGTGAGCAAACCAATT-3′



 


TaqMan Probe Name: MCM6-P








(SEQ ID NO:85)









Sequence: 5′-ACACAAGATTCGAGAGCTCACCTCATCCA-3′



 


MCM7:


Primer Name: MCM7_T1T3-F








(SEQ ID NO:25)









Sequence: CTCTGAGCCCGCCAAGC



 


Primer Name: MCM7_T1T3-R








(SEQ ID NO:26)









Sequence: TGTAAGAACTTCTTAACCTTTTCCTTCTCTA



 


Probe Name: MCM7_T1T3-Probe








(SEQ ID NO:27)









Sequence: CCCTCGGCAGCGATGGCACT



 


Primer Name: MCM7_T2T4-F








(SEQ ID NO:28)









Sequence: GAGGAATCCCGAGCTGTGAA



 


Primer Name: MCM7_T2T4-R








(SEQ ID NO:29)









Sequence: CCCGCTCCCGCCAT



 


Probe Name: MCM7_T2T4-Probe








(SEQ ID NO:30)









Sequence: CCCATGTGCTTCTTTGTTTACTAAGAGCGGAA



 


Primer Name: MCM7_T2-F








(SEQ ID NO:31)









Sequence: GTCCGAAGCCCCCAGAA



 


Primer Name: MCM7_T2-R








(SEQ ID NO:32)









Sequence: CCCGACAGAGACCACTCACA



 


Probe Name: MCM7_T2-Probe








(SEQ ID NO:33)









Sequence: CAGTACCCTGCTGAACTCATGCGCA



 


Primer Name: MCM7_T3T4-F








(SEQ ID NO:34)









Sequence: CGCTACGCGAAGCTCTTTG



 


Primer Name: MCM7_T3T4-R








(SEQ ID NO:35)









Sequence: CCTTTGTTTGCCATTGTTCTCTAA



 


Probe Name: MCM7_T3T4-Probe








(SEQ ID NO:36)









Sequence: TGCCGTACAAGAGCTGCTGCCTCA



 


TOPO2A:


Primer Name: TOP2A_F








(SEQ ID NO:86)









Sequence: 5′-GGCTACATGGTGGCAAGGA-3′



 


Primer Name: TOP2A_R








(SEQ ID NO:87)









Sequence: 5′-TGGAAATAACAATCGAGCCAAAG-3′



 


TaqMan Probe Name: TOP2A_P








(SEQ ID NO:88)









Sequence: 5′-TGCTAGTCCACGATACATCTTTACAATGCTCAGC-3′







Results

The results obtained for each biomarker are listed below in tabular form. The data is also summarized below.







TABLE 52







Snap-frozen Cervical Cancer Tissue Samples

















HPV

MCM6
MCM7
TOP2A


Patient
TPO ID
Path. Diag
Type
MCM2 TaqM
TaqMan
TaqM
TaqM

















Pt 01
CV-
Sq. Cell CA
HPV16
8.93
11.31
29.9
23.76



001


Pt 02
CV-
Adeno CA
HPV18
10.94
14.29
36.8
25.28



003


Pt 03
CV-
Adeno CA
HPV18
17.67
13.84
17.3
23.18



005


Pt 04
CV-
Sq. Cell CA
HPV16
23.61
13.3
18.77
23.26



007


Pt 05
CV-
Sq. Cell CA
HPV16
9.3
11.26
15.01
20.33



009


Pt 06
CV-
Sq. Cell CA
HPV16
13.86
11.58
7.37
8.37



011


Pt 07
CV-
Adeno CA
HPV18
27.03
16.32
19.74
34.29



013


Pt 08
CV-
Sq.Cell CA
HPV16,
8.28
8.16
3.65
8.57



015

HPV18, +


Pt 09
CV-
Sq. Cell CA
HPV18
12.61
13.56
20.07
11.31



017


Pt 10
CV-
Sq Cell CA
HPV18
31.88
23.38
21.17
27.48



019


Pt 11
CV-
Sq. Cell CA
HPV16
11.27
14.76
10.64
12.73



021


Pt 12
CV-
Sq. Cell CA
HPV16
11.39
11.29
32.17
21.11



023


Pt 13
CV-
Sq. Cell CA
HPV16
23.88
18.98
18.11
27.96



025


Pt 14
CV-
Sq. Cell CA
HPV18,
12.26
15.53
36.25
26.63



027

HPV16, +


Pt 15
CV-
Sq Cell
HPV16
6.56
7.92
9.64
7.81



029
Carcinoma


Pt 16
CV-
Sq Cell
HPV73
28.12
12.21
27.3
21.4



031
Carcinoma


Pt 17
CV-
Sq Cell
HPV16
8.76
7.59
14.37
12.42



033
Carcinoma


Pt 18
CV-
Sq Cell
HPV16
21.4
12.65
23.63
27.57



035
Carcinoma


Pt 19
CV-
Sq Cell
HPV18
12.59
13.06
14.37
9.24



037
Carcinoma


Pt 20
CV-
Adenosqu.
HPV16,
7.24
8.17
16.97
15.13



039
Cell CA
HPV18, +


Pt 21
CV-
Sq Cell CA
HPV16
9.61
11.84
13.88
11.92



041


Pt 22
CV-
Sq Cell CA
HPV16
21.57
13.21
18.31
24.19



043


Pt 23
CV-
Sq Cell CA
HPV16
21.19
13.18
18.76
19.97



045


Pt 24
CV-
Sq Cell CA
HPV18
24.61
19.09
20.19
28.14



047


Pt 25
CV-
Sq Cell CA
HPV18
11.43
10.2
13.70
10.55



049


Pt 26
CV-
Sq Cell CA
HPV16
24.25
20.54
23.26
33.26



051


Pt 27
CV-
Sq Cell CA
HPV45
26.74
21.34
20.96
20.34



053


Pt 28
CV-
Sq Cell CA
HPV16,
12.65
12
14.42
12.17



055

HPV18, +


Pt 29
CV-
Sq Cell CA
HPV16
16
14.72
25.46
22.16



057


Pt 30
CV-
Sq Cell CA
HPV16,
22.55
17.87
15.30
25.54



059

HPV18, +


Pt 31
CV-
Sq Cell CA
HPV16
24.08
21.88
23.11
25.28



061


Pt 32
CV-
Sq Cell CA
HPV18,
24.16
12.55
21.63
22.39



063

HPV16, +


Pt 33
CV-
Sq Cell CA
HPV16
26.63
16.05
27.56
28.84



065


Pt 34
CV-
Sq Cell CA
HPV16
19.61
23.28
19.03
25.57



067
















TABLE 53







Adjacent Normal Tissue Samples














TPO
HPV
MCM2
MCM6
MCM7
TOP2A


Patient
ID
Type
TaqM
TaqMan
TaqM
TaqM
















Pt 01
CV-
Negative
3.04
4.4
10.6
10.52



002


Pt 02
CV-
Negative
6.26
6.28
7.1
9.06



004


Pt 03
CV-
HPV18
2.06
2.53
2.14
3.86



006


Pt 04
CV-
Negative
3.14
4.15
4.8
8.03



008


Pt 05
CV-
Negative
2.2
3.45
5.07
6.91



010


Pt 06
CV-
Negative
2.06
2.29
7.34
6.82



012


Pt 07
CV-
Negative
N/A
N/A
N/A
N/A



014


Pt 08
CV-
Negative
2.55
3.13
3.72
2.02



016


Pt 09
CV-
Negative
2.09
3.09
4.74
1.24



018


Pt 10
CV-
Negative
8.15
6.76
5.42
10.41



020


Pt 11
CV-
Negative
4.53
5.34
4.33
6.64



022


Pt 12
CV-
Negative
1.94
2.45
9.03
6.13



024


Pt 13
CV-
Negative
N/A
N/A
N/A
N/A



026


Pt 14
CV-
Negative
2.62
2.95
10.38
5.3



028


Pt 15
CV-
Negative
1.14
1.28
2.06
1.54



030


Pt 16
CV-
Negative
N/A
N/A
N/A
N/A



032


Pt 17
CV-
Negative
1.24
1.91
1.32
0.42



034


Pt 18
CV-
Negative
3.4
1.89
4.01
4.32



036


Pt 19
CV-
Negative
3.48
4.98
5.60
7.92



038


Pt 20
CV-
Negative
1.84
3.28
3.73
1.38



040


Pt 21
CV-
Negative
1.53
3.3
4.77
1.01



042


Pt 22
CV-
Negative
2.65
4.03
2.74
2.59



044


Pt 23
CV-
Negative
3.09
3.53
5.90
3.42



046


Pt 24
CV-
HPV18
2.57
5.19
3.82
5.32



048


Pt 25
CV-
Negative
5.84
4.64
7.78
9.14



050


Pt 26
CV-
Negative
5.11
5.22
5.37
5.13



052


Pt 27
CV-
Negative
2.91
3.29
5.10
0.76



054


Pt 28
CV-
Negative
4.14
3.74
5.54
4.15



056


Pt 29
CV-
HPV16
2.83
4.98
10.13
7.57



058


Pt 30
CV-
Negative
6.41
5
5.39
10.05



060


Pt 31
CV-
Negative
5.72
4.93
9.29
9.95



062


Pt 32
CV-
Negative
8.06
5.41
7.64
9



064


Pt 33
CV-
Negative
9.93
7.94
10.78
9.95



066


Pt 34
CV-
Negative
2.36
6.39
5.73
1.81



068









Summary of Results







TABLE 54







Tumor vs adjacent normal











Marker
Tumor (M ± SD)
Normal (M ± SD)
R
P





MCM2
17.43 ± 7.34
3.71 ± 2.21
4.70
<0.0001


MCM6
14.32 ± 4.32
4.12 ± 1.56
3.48
<0.0001


MCM7
19.38 ± 6.94
5.85 ± 2.59
3.31
<0.0001


TOP2A
20.53 ± 7.54
5.56 ± 3.33
3.69
<0.0001





M: Mean;


SD: Standard Deviation;


R: Ratio of the means of tumor versus normal;


P: P value of t-test.













TABLE 55







HPV-16 vs HPV-18











Marker
Tumor HPV type
Cases
Tumor (M ± SD)
Normal (M ± SD)














MCM2
16
18
16.77 ± 6.78
3.29 ± 2.13



18
8
17.23 ± 8.16
3.99 ± 2.40



16 + 18
6
14.52 ± 7.18
4.27 ± 2.47


MCM6
16
18
14.19 ± 4.44
3.97 ± 1.75



18
8
14.24 ± 4.10
4.35 ± 1.54



16 + 18
6
12.38 ± 3.89
3.92 ± 1.04


MCM7
16
18
19.39 ± 6.94
6.07 ± 2.98



18
8
17.23 ± 4.16
5.07 ± 1.91



16 + 18
6
18.04 ± 7.71
6.07 ± 2.56


TOP2A
16
18
20.92 ± 7.38
5.46 ± 3.26



18
8
19.78 ± 9.52
6.19 ± 3.33



16 + 18
6
18.41 ± 7.49
5.32 ± 3.57
















TABLE 56







Squamous Cell Carcinoma vs Adenocarcinoma











Marker
Histopathology
Cases
Tumor (M ± SD)
Normal (M ± SD)














MCM2
SCC
30
17.66 ± 7.28
3.74 ± 2.23



AC
4
15.72 ± 8.69
3.39 ± 2.49


MCM6
SCC
30
14.48 ± 4.44
4.13 ± 1.55



AC
4
13.16 ± 3.49
4.03 ± 1.98


MCM7
SCC
30
19.27 ± 7.25
6.01 ± 2.58



AC
4
20.20 ± 4.57
4.32 ± 2.53


TOP2A
SCC
30
20.01 ± 7.47
5.65 ± 3.34



AC
4
21.47 ± 7.87
4.77 ± 3.92





SCC: Squamous Cell Carcinoma;


AC: Adenocarcinoma.






Example 12
Real-Time PCR Detection of Biomarkers in Cervical and Breast Cancer Cell Lines
TaqMan® real-time PCR was performed to detect MCM2, MCM6 and MCM7 expression levels in cervical and breast cancer cell lines.
Experimental Design and Protocols
Three human cervical cancer cell lines of SiHa, Caski and HeLa and three human breast cancer cell lines of MCF-7, SK-BR3 and CAMA were purchased from ATCC and used in this experiment. Total cellular RNA was extracted from freshly cultured cells by RNeasy® Protect Mini kit (Qiagen, Valencia, Calif.) and converted into the single stranded cDNA form with random hexamers using the High-Capacity cDNA Archive Kit (Applied Biosystems, P/N: 4322171). Real-time PCR was performed on the ABI Prism® 7700 Sequence Detection System using TaqMan® Universal PCR Master Mix (Applied Biosystems, Inc., Foster City, Calif.).
The primers and probes for specific amplification of MCM2, MCM6 and MCM7 were designed with ABI Primer ExpressTM program, v1.5. MCM7 contains four transcriptional variants: transcript variant 1 (T1, refseq NM—005916) and transcript variant 2 (T2, refseq NM—182776) were identified in NCBI Entrez nucleotide database. Variant T3 and T4 have alternate exons near the 5′-end as analyzed by EST assembly through NCBI's Model Maker. Primers and probes were designed as T1T3, T2T4, T2 and T3T4 specifically for detecting variants T1 and T3, T2 and T4, T2, and T3 and T4, respectively. The sequences of primers and probes are shown above in Example 10 and 11.
The probes were labeled with a fluorescent dye FAM (6-carboxyfluorescein) on the 5′ base, and a quenching dye TAMRA (6-carboxytetramethylrhodamine) on the 3′ base. 18S ribosomal RNA was utilized as endogenous control. 18S rRNA probe was labeled with a fluorescent dye VIC. Pre-developed 18S rRNA primer/probe mixture was purchased from Applied Biosystems. 10 ng of cDNA were applied to the reaction mixture containing 0.9 μM and 0.25 μM of the primers and probes, respectively, in a total volume of 25 μl. The amplification conditions were: 2 minutes at 50° C., 10 minutes at 95° C., and a two-steps cycle of 95° C. for 15 seconds and 60° C. for 60 seconds, for a total of 40 cycles. At least three no-template control reaction mixtures were included in each run. All experiments were performed in duplicate. The relative quantification method was employed to calculate the expression levels of target genes relative to the 18S endogenous control, based on their CT values following the ABI's user manual (P/N 4303859).
Results
The results obtained for each biomarker are listed below in tabular form.







TABLE 57







Biomarker Expression Cervical and Breast Cancer Cell Lines














SiHa
Caski
HeLa
MCF7
SK-BR3
CAMA
















MCM2
21.4
5.01
8.79
18.84
7.65
17.32


MCM6
12.34
5.77
6.46
12.6
5.44
13.14


MCM7
20.53
17.27
8.31
26.91
30.38
25.36









Conclusions

The cervical HeLa cell line was shown to have low-expression levels of MCM2, MCM6 and MCM7 biomarkers. The cervical SiHa, breast MCM7, and CAMA cell lines all showed overexpression of MCM2, MCM6 and MCM7 biomarkers. Cervical Caski and breast SK-BR3 cell lines showed overexpression of MCM7, but low-expression for MCM2 and MCM6.
Example 13
Induction of Cervical Biomarker Expression in 293 Cells by Transient HPV16 E6/E7 Gene Transfection
TaqMan® real-time PCR assay was used to investigate the linkage of cervical biomarker expression with high-risk HPV oncogene transcription in an HEK 293 cell line system.
Experimental Design and Protocols
A tetracycline regulated expression system (T-Rex system, Invitrogen, Inc) was adapted in this experiment. T-Rex vectors expressing HPV16 E2, E6 or E7 protein were constructed. Vectors containing mutant E2, E6 or E7 genes were utilized as negative controls. T-Rex 293 cells were then transfected with the HPV plasmids, and expression of HPV genes were activated by tetracycline for 4 hours, 24 hours and 72 hours. Total cellular RNA was extracted from the transfected cells by RNeasy® Protect Mini kit (Qiagen, Valencia, Calif.) and converted into the single stranded cDNA form with random hexamers using the High-Capacity cDNA Archive Kit (Applied Biosystems, P/N: 4322171). Real-time PCR was performed on the ABI Prism® 7700 Sequence Detection System using TaqMan® Universal PCR Master Mix (Applied Biosystems, Inc., Foster City, Calif.).
The primers and probes for specific amplification of MCM2, MCM6, MCM7, TOP2A, Cyclin E1, p21, p14, HPV16E2, E6 and E7 were designed with ABI Primer ExpressTM program, v1.5. MCM7 contains four transcriptional variants: transcript variant 1 (T1, refseq NM—005916) and transcript variant 2 (T2, refseq NM—182776) were identified in NCBI Entrez nucleotide database. Variant T3 and T4 have alternate exons near the 5′-end as analyzed by EST assembly through NCBI's Model Maker. Primers and probes were designed as T1T3, T2T4, T2 and T3T4 specifically for detecting variants T1 and T3, T2 and T4, T2, and T3 and T4, respectively. The sequences of primers and probes are shown as shown in Examples 10 and 11.
The probes were labeled with a fluorescent dye FAM (6-carboxyfluorescein) on the 5′ base, and a quenching dye TAMRA (6-carboxytetramethylrhodamine) on the 3′ base. 18S ribosomal RNA was utilized as endogenous control. 18S rRNA probe was labeled with a fluorescent dye VIC. Pre-developed 18S rRNA primer/probe mixture was purchased from Applied Biosystems. 10 ng of cDNA were applied to the reaction mixture containing 0.9 μM and 0.25 μM of the primers and probes, respectively, in a total volume of 25 μl. The amplification conditions were: 2 minutes at 50° C., 10 minutes at 95° C., and a two-steps cycle of 95° C. for 15 seconds and 60° C. for 60 seconds, for a total of 40 cycles. At least three no-template control reaction mixtures were included in each run. All experiments were performed in duplicate. The relative quantification method was employed to calculate the expression levels of target genes relative to the 18S endogenous control, based on their CT values following the ABI's user manual (P/N 4303859).
Results
Expression of HPV16 E2, E6 and E7 genes in T-Rex 293 cells was observed to increase through the time-course of transfection. mRNA expression of Topo2A, MCM2, MCM6, MCM7 and cyclin E in T-Rex 293 cells was significantly induced by HPV16 E6 or E7 genes, post-transfection from 4 hours up to 72 hours. However, there were no elevated expression levels detected for p21 and p14 post HPV gene transfection. Expression of E6 or E7 did not appear to be repressed by co-transfection of E2 gene. This is because the expression of E6 or E7 was purely driven by the external CMV promoter instead of the natural HPV promoters. The latter are not present in this model system.







TABLE 58







Topo2A

















0 h

4 h



72 h


Transfection
0 h
SD
4 h
SD
24 h
24 h SD
72 h
SD


















293-H16E2
6.91
0.07
5.22
0.13
5.68
0.14
6.61
0.36


293-H16E6
6.91
0.07
11.31
0.22
18.13
0.89
17.39
0.85


293-H16E7
6.91
0.07
20.33
0.9
28.94
0.71
35.02
1.03


293-
6.91
0.07
6.43
0.35
8.18
0.64
7.39
0.18


H16dE7


293-LacZ
6.91
0.07
7.4
0.07
7.36
0.22
7.25
0.67
















TABLE 59







MCM2

















0 h

4 h



72 h


Transfection
0 h
SD
4 h
SD
24 h
24 h SD
72 h
SD


















293-H16E2
4.79
0.23
5.25
0.36
5.24
0.31
4.44
0.3


293-H16E6
4.79
0.23
6.04
0.21
9.38
0.37
12.08
0.18


293-H16E7
4.79
0.23
10.81
0.16
12.29
0.36
16.34
0.8


293-
4.79
0.23
5.72
0.36
4.98
0.27
5.03
0.39


H16dE7


293-LacZ
4.79
0.23
5.67
0.61
5.68
0.47
5.98
0.79
















TABLE 60







MCM6



















4 h

24 h

72 h


Transfection
0 h
0 h SD
4 h
SD
24 h
SD
72 h
SD


















293-H16E2
3.62
0.2
3.5
0.22
4.72
0
4.44
0.26


293-H16E6
3.62
0.2
4.74
0.07
9.03
0.04
9.68
0.43


293-H16E7
3.62
0.2
7.7
0.04
13.5
0.33
14.03
0.41


293-
3.62
0.2
5.23
0.28
4.6
0.32
4.73
0.37


H16dE7


293-LacZ
3.62
0.2
4.77
0.12
4.66
0.14
5.34
0.39
















TABLE 61







MCM7

















0 h





72 h


Transfection
0 h
SD
4 h
4 h SD
24 h
24 h SD
72 h
SD


















293-H16E2
4.2
0.04
6.3
0.28
5.3
0.18
5.8
0.31


293-H16E6
4.2
0.04
4.99
0.05
9.55
0.23
15.24
0.3


293-H16E7
4.2
0.04
10.11
0.84
14.23
0.84
21.18
0.31


293-
4.2
0.04
3.65
0.3
6.06
0.3
4.64
0.07


H16dE7


293-LacZ
4.2
0.04
5.74
0.45
5.31
0.55
5.66
0.17
















TABLE 62







Cyclin E1

















0 h



24 h

72 h


Transfection
0 h
SD
4 h
4 h SD
24 h
SD
72 h
SD


















293-H16E2
6.02
0.00
5.06
0.10
5.03
0.35
5.72
0.31


293-H16E6
6.02
0.00
9.19
0.18
8.95
0.79
9.38
0.18


293-H16E7
6.02
0.00
12.91
0.38
17.63
0.17
17.32
0.25


293-
6.02
0.00
5.45
0.24
6.87
0.20
5.11
0.08


H16dE7


293-LacZ
6.02
0.00
5.72
0.31
6.28
0.37
5.65
0.64
















TABLE 63







p21

















0 h



24 h

72 h


Transfection
0 h
SD
4 h
4 h SD
24 h
SD
72 h
SD





293-H16E2
4.76
0.19
4.05
0.30
5.19
0.61
4.92
0.60


293-H16E6
4.76
0.19
5.56
0.19
5.60
0.08
7.21
0.07


293-H16E7
4.76
0.19
7.52
0.29
5.22
0.13
6.45
0.13


293-
4.76
0.19
4.38
0.26
5.60
0.66
5.10
0.05


H16dE7


293-LacZ
4.76
0.19
3.86
0.00
4.53
0.27
5.37
0.29
















TABLE 64







p14















Transfection
0 h
0 h SD
4 h
4 h SD
24 h
24 h SD
72 h
72 h SD





293-H16E2
4.78
0.30
4.44
0.09
5.04
0.44
5.04
0.07


293-H16E6
4.78
0.30
4.77
0.12
5.48
0.13
4.52
0.11


293-H16E7
4.78
0.30
6.38
0.62
5.60
0.25
6.43
0.35


293-H16dE7
4.78
0.30
5.08
0.12
5.53
0.35
5.10
0.15


293-LacZ
4.78
0.30
4.54
0.40
4.68
0.16
5.76
0.25
















TABLE 65







HPV16 E2




















E2
E6
E7
dE2
dE6
dE7
E2 + E6
E2 + E7
dE2 + E6
dE2 + E7
LacZ
Mock























 4 h
130.22
0
0
110.7
0
0
95.34
36.6
3.94
12.86
0
0


24 h
162.12
0
0
111.41
0
0
118.17
90.19
19.77
7.7
0
0


72 h
251.55
0
0
141.57
0
0
162.54
128.41
32.94
9.89
0
0
















TABLE 66







HPV16 E6




















E2
E6
E7
dE2
dE6
dE7
E2 + E6
E2 + E7
dE2 + E6
dE2 + E7
LacZ
Mock























 4 h
0
205
0
0
219.87
0
128.41
0
199.65
0
0
0


24 h
0
329.67
0
0
225.96
0
158.31
0
188.03
0
0
0


72 h
0
757.26
0
0
315.22
0
392
0
271.55
0
0
0
















TABLE 67







HPV16 E7




















E2
E6
E7
dE2
dE6
dE7
E2 + E6
E2 + E7
dE2 + E6
dE2 + E7
LacZ
Mock























 4 h
0
0
330.76
0
0
165.48
0
120.65
0
201.19
0
0


24 h
0
0
1514.6
0
0
239.63
0
857.89
0
600.57
0
0


72 h
0
0
2806.8
0
0
355.9
0
1444.25
0
809.11
0
0









Example 14
Increasing Antigen Accessibility in Immunocytochemistry and Immunohistochemistry Methods Using a Slide Pretreatment Buffer
Specimen Selection and Reagent Description
Paired cytology and histology specimens, from the same patient, were subjected to immunoassays to detect biomarker overexpression. Paraffin block tissue samples and SurePath® cytology specimens from patients categorized as ASCUS (3), LSIL (6), and HSIL (5) were analyzed. The reagents used were the Antibody Cocktail (for cytology), the Modified Antibody Cocktail (for histology), Detection Reagents, Counterstains, and SureSlide® Preparation Buffer 10× (pretreatment buffer).
Cytology Slide Preparation and Automated Immunocytochemistry
For immunocytochemistry, slide preparation and pretreatment was conducted as indicated in Example 5. Automated immunocytochemistry was then performed on each cytology specimen as described in Example 5 with one exception. The primary antibody cocktail (MCM2 Clone 26H6.19 1:10,000, MCM2 Clone 27C5.6 1:800, TOPOIIA Clone SWT3D1 1:1000) incubation was reduced to 30 minutes for this experiment.
Histology Slide Preparation and Automated Immunohistochemistry
For each case, 4 micron sections were cut and dried overnight or for 20 minutes in a 70° C. forced air oven. Sections were deparaffinized in 3 changes of xylene for 5 minutes each. Slides were then cleared in absolute alcohol for 5 minutes each. Slides were brought down to water and rinsed thoroughly. Slides were transferred to a preheated solution of 1× SureSlide Preparation Buffer and incubated in the steamer for 25 minutes. The slides were removed from the steamer and allowed to cool at room temperature for 20 minutes. Slides were slowly rinsed in water until the buffer was completely exchanged. A TBST rinse was applied for 2 changes at 2 minutes each.
Automated immunohistochemistry was conducted as described in Example 5 for immunocytochemistry, with two exceptions. The primary antibody cocktail incubation was reduced to 30 minutes for this experiment. Additionally, the primary antibody cocktail was modified with the following dilutions (MCM2 Clone 26H6.19 1:4,000, MCM2 Clone 27C5.6 1:200, TOPOIIA Clone SWT3D1 1:400).
Results
The anticipated staining patterns were observed on both the histology and cytology specimens with the use of the RUO reagents. Specifically, the ability to immunostain both histology and cytology specimens with the SureSlide® Preparation Buffer, Detection Reagents and the Counterstain Reagents was successfully demonstrated.







TABLE 68







Biomarker Nucleotide and Amino Acid Sequence Information










Nucleotide Sequence
Amino Acid Sequence












Accession
Sequence
Accession
Sequence


Biomarker Name
No.
Identifier
No.
Identifier





Cyclin E1 (Isoform 1)
NM_001238
SEQ ID NO: 1
NP_001229
SEQ ID NO: 2


Cyclin E1 (Isoform 2)
NM_057182
SEQ ID NO: 3
NP_476530
SEQ ID NO: 4


Cyclin E2 (Isoform1)
NM_057749)
SEQ ID NO: 5
NP_477097
SEQ ID NO: 6


Cyclin E2 (Isoform 2)
NM_057735
SEQ ID NO: 7
NP_477083
SEQ ID NO: 8


Cyclin E2 (Isoform 3)
NM_004702
SEQ ID NO: 9
NP_004693
SEQ ID NO: 10


MCM2
NM_004526
SEQ ID NO: 11
NP_0045417
SEQ ID NO: 12


MCM6
NM_005915
SEQ ID NO: 89
NP_005906
SEQ ID NO: 90


MCM7 (Isoform 1)
NM_005916
SEQ ID NO: 13
NP_005907
SEQ ID NO: 14


MCM7 (Isoform 2)
NM_182776
SEQ ID NO: 15
NP_877577
SEQ ID NO: 16


p21/waf1 (Variant 1)
NM_000389
SEQ ID NO: 17
NP_000380
SEQ ID NO: 18


p21/waf1 (Variant 2)
NM_078467
SEQ ID NO: 19
NP_510867
SEQ ID NO: 20


p14ARF
NM_058195
SEQ ID NO: 21
NP_478102
SEQ ID NO: 22


Topo2a
NM_001067
SEQ ID NO: 23
NP_0010568
SEQ ID NO: 24









In light of the above description and examples, one skilled in the art will appreciate that the methods of the invention permit superior detection of high-grade cervical disease, independent of age, in comparison to conventional practice. The methods of the invention may find particular use as described below:

    
    
        For women over the age of thirty, the test may be a reflex from either an HPV positive result or as a reflex from an ASCUS+ cytology result.
        For women under the age of 30, the test may be used in combination with cytology for the detection of high-grade cervical disease.
        For women over the age of 30, the test may be used in combination with cytology for the detection of high-grade cervical disease.
        For women under the age of 30, the test may be used as a primary screen to detect high-grade cervical disease.
        For women over the age of 30, the test may be used as a primary screen to detect high-grade cervical disease.
        The test may be a replacement for the Pap smear in women under the age of thirty.
        Ultimately, the test may be a replacement for the Pap smear, independent of age.
    
    


Other potential advantages stemming from the practice of the present invention include:

    
    
        Detection of histologic high-grade abnormality in women 30 years old and above with NIL/HPV positive results.
        Superior specificity for the detection of high-grade cervical disease in women over the age of 30 who are positive to the DNA+Pap test.
        Superior detection for high-grade cervical disease in women within the ASC-US, ASC-H, and LSIL categories, independent of age.
        Superior specificity for the detection of high-grade cervical within HSIL category.
        Detection of high-grade cervical disease in conjunction with cytology-based diagnosis in women under the age of 30.
        Detection of high-grade cervical disease in conjunction with cytology-based diagnosis, independent of age.
        Improved specificity for the detection of high-grade cervical disease as a primary screen in women under the age of 30.
        Improved specificity for the detection of high-grade cervical disease as a primary screen, independent of age.
        Identification of cervical disease and differentiation of HPV infection and high-grade cervical disease.
        Acceptable assay performance can be established using manual interpretation or assisted interpretation via automated microscopy.
    
    


All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended embodiments.

## Claims

1. A method for diagnosing high-grade cervical disease in a patient independent of the patient's HPV infection status comprising detecting overexpression of at least one nucleic acid molecule that encodes a nuclear biomarker that is selectively overexpressed in high-grade cervical disease, wherein the nuclear biomarker is selected from the group consisting of p14ARF, p21waf1, Topo2A, and Cyclin E, the method comprising:
(a) obtaining a body sample from the patient;
(b) isolating nucleic acid material from the sample;
(c) mixing said nucleic acid material with at least one pair of oligonucleotide primers specific for the nuclear biomarker and a thermostable DNA polymerase under conditions that are suitable for amplification by polymerase chain reaction (PCR);
d) performing PCR; and,
e) detecting PCR amplification products.

2. The method of claim 1, wherein performing PCR comprises performing RT-PCR.

3. The method of claim 1, wherein the method is performed in conjunction with morphological analysis.

4. The method of claim 1, wherein the sample comprises cervical cells in suspension in a liquid-based preparation.

5. The method of claim 1, wherein the sample comprises a cervical tissue sample.

6. The method of claim 1, wherein the method is performed in response to the patient having an abnormal Pap smear result.

7. The method of claim 1, wherein the method is performed as a primary screen for high-grade cervical disease in a general patient population.

8. The method of claim 1, wherein the method if performed in conjunction with Papanicolaou (Pap) staining of a cervical sample from the patient.