Gene expression profile of cervical tissue compared to exfoliated cells: impact on biomarker discovery

c-myc copy number gain is a powerful prognosticator of disease outcome in cervical dysplasia

Cervical carcinoma develops from preneoplasia by a multistep process. Although most low-grade dysplastic lesions will regress without intervention and even high-grade changes exhibit a substantial rate of regression, a small percentage of dysplasia will progress over time. Thus, indicators are needed to estimate the biological risk and to help avoid overtreatment in women who desire to preserve fertility. In addition to the classical biomarkers, PCR-ELISA-determined HPV genotype and immunohistochemically assessed p16^INK4a and Ki-67 expression, cells with integrated HPV and copy number gain of TERC and c-myc were quantified in a panel of 104 benign, intraepithelial neoplastic (CIN I, II, III) and cancerous lesions using fluorescence in situ hybridization. Optimal cut-off values were calculated; Kaplan-Meier curves and a Cox proportional hazard regression model were used to evaluate prognostic signatures. The assay reliably identified HPV integration, TERC and c-myc copy number gain as determined by comparisons with established biomarkers. All biomarker levels increased with the progression of the disease. However, only c-myc copy number gain independently prognosticated a low probability of dysplastic regression. Our results suggest that c-myc plays a key role in the process of dysplastic transformation and might thus be exploited for treatment and follow-up decision-making of cervical dysplasia.

Survival of exfoliated epithelial cells: a delicate balance between anoikis and apoptosis

The recovery of exfoliated cells from biological fluids is a noninvasive technology which is in high demand in the field of translational research. Exfoliated epithelial cells can be isolated from several body fluids (i.e., breast milk, urines, and digestives fluids) as a cellular mixture (senescent, apoptotic, proliferative, or quiescent cells). The most intriguing are quiescent cells which can be used to derive primary cultures indicating that some phenotypes retain clonogenic potentials. Such exfoliated cells are believed to enter rapidly in anoikis after exfoliation. Anoikis can be considered as an autophagic state promoting epithelial cell survival after a timely loss of contact with extracellular matrix and cell neighbors. This paper presents current understanding of exfoliation along with the influence of methodology on the type of gastrointestinal epithelial cells isolated and, finally, speculates on the balance between anoikis and apoptosis to explain the survival of gastrointestinal epithelial cells in the environment.

Exfoliative cytology for diagnosing oral cancer

Exfoliative cytology is a minimally invasive technique for obtaining oral cell specimens from patients for diagnostic purposes. Classical applications of oral cytology studies, such as oral candidiasis, have been extended to include oral precancerous and cancerous lesions. A number of analytical methods are available for studying cytology specimens. The development of molecular analysis techniques, the oral cancer etiopathogenic process, and improvements in liquid-based exfoliative cytology are leading to renewed interest in exfoliative cytology. Results sometimes are disputed, so the aim of our review was to clarify the applicability of exfoliative cytology to the diagnosis of oral precancerous and cancerous lesions.

Exfoliated epithelial cells: potentials to explore gastrointestinal maturation of preterm infants

Exfoliated epithelial cells represent valuable source of information on the physiopathological state of the mucosa. However, the interpretation of data obtained from exfoliated cells is complicated by the conditions of isolation as well as the health of the subject. Exfoliation is either: a) a natural loss of body cells implying a molecular signal related to the turnover of terminally differentiated cells and to the progressive mobilization of proliferative as well as stem cells or b) the result of manual exfoliation by applying mechanical constraints like scraping. Depending on the methodology of isolation, exfoliated epithelial cells are believed to be either in apoptosis or in anoïkis. Most studies are using microscopic examination to demonstrate the presence of typical cells along with measurements on a limited number of biomarkers. Only few studies using proteomics or transcriptomics are available and they open discussion about tissue references and normalization. The main advantage of measures realized on exfoliated epithelial cells is that they are strictly non-invasive and open the possibility to evaluate maturation of gastric and intestinal tissues in long-term experiments performed on the same animal or in translational research on samples recovered from preterm infants.

Gene expression changes during HPV-mediated carcinogenesis: a comparison between an in vitro cell model and cervical cancer

We used oligonucleotide microarrays to investigate gene expression changes associated with multi-step human papillomavirus type 16 (HPV16)-mediated carcinogenesis in vitro. Gene expression profiles in 4 early passage HPV16-immortalized human keratinocyte (HKc) lines derived from different donors were compared with their corresponding 4 late-passage, differentiation-resistant cell lines, and to 4 pools of normal HKc, each composed of 3 individual HKc strains, on Agilent 22 k human oligonucleotide microarrays. The resulting data were analyzed using a modified T-test coded in R to obtain lists of differentially expressed genes. Gene expression changes identified in this model system were then compared with gene expression changes described in published studies of cervical intraepithelial neoplasia (CIN) and cervical cancer. Common genes in these lists were further studied by cluster analysis. Genes whose expression changed in the same direction as in CIN or cervical cancer (concordant) at late stages of HPV16-mediated transformation in vitro formed one major cluster, while those that changed in the opposite direction (discordant) formed a second major cluster. Further annotation found that many discordant expression changes involved gene products with an extracellular localization. Two novel genes were selected for further study: overexpression of SIX1 and GDF15, observed during in vitro progression in our model system, was confirmed in tissue arrays of cervical cancer. These microarray-based studies show that our in vitro model system reflects many cellular and molecular alterations characteristic of cervical cancer, and identified SIX1 and GDF15 as 2 novel potential biomarkers of cervical cancer progression.

RNA from brush oral cytology to measure squamous cell carcinoma gene expression

BACKGROUND

RNA expression analysis of oral keratinocytes can be used to detect early stages of disease such as oral cancer or to monitor on-going treatment responses of the same or other oral diseases. A limitation is the inability to obtain high quality RNA from oral tissue without using biopsies. While oral cytology cell samples can be obtained from patients in a minimally invasive manner they have not been validated for quantitative analysis of RNA expression.

METHODS

As a starting point in the analysis of tumor markers in oral squamous cell carcinoma (OSCC), we examined RNA in brush cytology samples from hamsters treated with dibenzo[a,l]pyrene to induce oral carcinoma. Three separate samples from each animal were assessed for expression of candidate marker genes and control genes measured with real-time RT-PCR.

RESULTS

Brush oral cytology samples from normal mucosa were shown to consist almost exclusively of epithelial cells. Remarkably, ss-2 microglobulin and cytochrome p450, 1B1 (CYP1B1) RNA showed potential utility as markers of OSCC in samples obtained in this rapid and non-surgical manner.

CONCLUSION

Brush oral cytology may prove useful as a source of RNA for gene expression analysis during the progression of diseases of the oral epithelium such as OSCC.

Comprehensive serial analysis of gene expression of the cervical transcriptome

Background

More than half of the approximately 500,000 women diagnosed with cervical cancer worldwide each year will die from this disease. Investigation of genes expressed in precancer lesions compared to those expressed in normal cervical epithelium will yield insight into the early stages of disease. As such, establishing a baseline from which to compare to, is critical in elucidating the abnormal biology of disease. In this study we examine the normal cervical tissue transcriptome and investigate the similarities and differences in relation to CIN III by Long-SAGE (L-SAGE).

Results

We have sequenced 691,390 tags from four L-SAGE libraries increasing the existing gene expression data on cervical tissue by 20 fold. One-hundred and eighteen unique tags were highly expressed in normal cervical tissue and 107 of them mapped to unique genes, most belong to the ribosomal, calcium-binding and keratinizing gene families. We assessed these genes for aberrant expression in CIN III and five genes showed altered expression. In addition, we have identified twelve unique HPV 16 SAGE tags in the CIN III libraries absent in the normal libraries.

Conclusion

Establishing a baseline of gene expression in normal cervical tissue is key for identifying changes in cancer. We demonstrate the utility of this baseline data by identifying genes with aberrant expression in CIN III when compared to normal tissue.

Evaluation of RNA markers for early detection of cervical neoplasia in exfoliated cervical cells

Numerous molecular biomarkers have been suggested for early detection of cervical cancer, but their usefulness in routinely collected exfoliated cells remains uncertain. We used quantitative reverse transcription-PCR to evaluate expression of 40 candidate genes as markers for high-grade cervical intraepithelial neoplasia (CIN) in exfoliated cervical cells collected at the time of colposcopy. Samples from the 93 women with CIN3 or cancer were compared with those from 186 women without disease matched (1:2) for age, race, and high-risk human papillomavirus status. Normalized threshold cycles (C(t)) for each gene were analyzed by receiver operating characteristics to determine their diagnostic performance in a split sample validation approach. Six markers were confirmed by an area under the curve >0.6 in both sample sets: claudin 1 (0.75), minichromosome maintenance deficient 5 (0.71) and 7 (0.64), cell division cycle 6 homologue (0.71), antigen identified by monoclonal antibody Ki-67 (0.66), and SHC SH2-domain binding protein 1 (0.61). The sensitivity for individual markers was relatively low and a combination of five genes to a panel resulted in 60% sensitivity with 76% specificity, not positively increasing this performance. Although the results did not indicate superiority of RNA markers for cervical cancer screening, their performance in detecting disease in women referred for colposcopy suggests that the genes and pathways they highlight could be useful in alternative detection formats or in combination with other screening indicators.

DNA methylation profile at the DNMT3L promoter: a potential biomarker for cervical cancer

Epigenetic events play a prominent role during cancer development. This is evident from the fact that almost all cancer types show aberrant DNA methylation. These abnormal DNA methylation levels are not restricted to just a few genes but affect the whole genome. Previous studies have shown genome-wide DNA hypomethylation and gene-specific hypermethylation to be a hallmark of most cancers. Molecules like DNA methyltransferase act as effectors of epigenetic reprogramming. In the present study we have examined the possibility that the reprogramming genes themselves undergo epigenetic modifications reflecting their changed transcriptional status during cancer development. Comparison of DNA methylation status between the normal and cervical cancer samples was carried out at the promoters of a few reprogramming molecules. Our study revealed statistically significant DNA methylation differences within the promoter of DNMT3L. A regulator of de novo DNA methyltransferases DNMT3A and DNMT3B, DNMT3L promoter was found to have lost DNA methylation to varying levels in 14 out of 15 cancer cervix samples analysed. The present study highlights the importance of DNA methylation profile at DNMT3L promoter not only as a promising biomarker for cervical cancer, which is the second most common cancer among women worldwide, but also provides insight into the possible role of DNMT3L in cancer development.

Molecular targets in gynaecological cancers

The application of high throughput expression profiling and other advanced molecular biology laboratory techniques has revolutionised the management of cancers and is gaining attention in the field of gynaecological cancers. Such new approaches may help to improve our understanding of carcinogenesis and facilitate screening and early detection of gynaecological cancers and their precursors. Individualised prediction of patients' responses to therapy and design of personalised molecular targeted therapy is also possible. The studies of various molecular targets involved in the various signal pathways related to carcinogenesis are particularly relevant to such applications. At the moment, the application of detection and genotyping of human papillomavirus in management of cervical cancer is one of the most well established appliances of molecular targets in gynaecological cancers. Methylation, telomerase and clonality studies are also potentially useful, especially in assisting diagnosis of difficult clinical scenarios. This post-genomic era of clinical medicine will continue to make a significant impact in routine pathology practice. The contribution of pathologists is indispensable in analysis involving tissue microarray. On the other hand, both pathologists and bedside clinicians should be aware of the limitation of these molecular targets. Interpretation must be integrated with clinical and histopathological context to avoid misleading judgement. The importance of quality assurance of all such molecular techniques and their ethical implications cannot be over-emphasised.

Individualized markers optimize class prediction of microarray data

Background

Identification of molecular markers for the classification of microarray data is a challenging task. Despite the evident dissimilarity in various characteristics of biological samples belonging to the same category, most of the marker – selection and classification methods do not consider this variability. In general, feature selection methods aim at identifying a common set of genes whose combined expression profiles can accurately predict the category of all samples. Here, we argue that this simplified approach is often unable to capture the complexity of a disease phenotype and we propose an alternative method that takes into account the individuality of each patient-sample.

Results

Instead of using the same features for the classification of all samples, the proposed technique starts by creating a pool of informative gene-features. For each sample, the method selects a subset of these features whose expression profiles are most likely to accurately predict the sample's category. Different subsets are utilized for different samples and the outcomes are combined in a hierarchical framework for the classification of all samples. Moreover, this approach can innately identify subgroups of samples within a given class which share common feature sets thus highlighting the effect of individuality on gene expression.

Conclusion

In addition to high classification accuracy, the proposed method offers a more individualized approach for the identification of biological markers, which may help in better understanding the molecular background of a disease and emphasize the need for more flexible medical interventions.

DNA and RNA references for qRT-PCR assays in exfoliated cervical cells

The noncritical use of housekeeping genes, RNA mass, or cell number for normalization in quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assays has come under scrutiny in recent years, highlighting the need to evaluate references in the immediate context of the relevant samples and experimental design. The purpose of this study was to select appropriate references for normalizing qRT-PCR assays of gene expression in exfoliated cervical cells. We used total nucleic acid extracts from 30 samples, representing the full spectrum of pre-invasive cervical neoplasia. We determined the DNA content by quantitative PCR for the single-copy gene beta-globin and total RNA content using quantitative image analysis of ribosomal bands. In addition, qRT-PCR for 13 candidate housekeeping genes was performed. We used two analysis methods, geNorm and Norm-Finder, to identify the best combination of reference genes and then correlated housekeeping gene expression with DNA content and gel representation of ribosomal RNA. ACTB was the most stable single gene. The addition of PGK1 and RPLP0 increased the robustness in qRT-PCR applications not stratified by disease. These genes also showed the highest correlation with DNA contents in the same samples. If special attention to intraepithelial lesions is appropriate, RPL4 and PGK1 are recommended as the best combination of two genes.