Overview of microarray analysis of gene expression and its applications to cervical cancer investigation

RNA Sequencing of Carboplatin- and Paclitaxel-Resistant Endometrial Cancer Cells Reveals New Stratification Markers and Molecular Targets for Cancer Treatment

Despite advances in surgical technique and adjuvant treatment, endometrial cancer has recently seen an increase in incidence and mortality in the USA. The majority of endometrial cancers can be cured by surgery alone or in combination with adjuvant chemo- or radiotherapy; however, a subset of patients experience recurrence for reasons that remain unclear. Recurrence is associated with chemoresistance to carboplatin and paclitaxel and consequentially, high mortality. Understanding the pathways involved in endometrial cancer chemoresistance is paramount for the identification of biomarkers and novel molecular targets for this disease. Here, we generated the first matched pairs of carboplatin-sensitive/carboplatin-resistant and paclitaxel-sensitive/paclitaxel-resistant endometrial cancer cells and subjected them to bulk RNA sequencing analysis. We found that 45 genes are commonly upregulated in carboplatin- and paclitaxel-resistant cells as compared to controls. Of these, the leukemia inhibitory factor, (LIF), the protein tyrosine phosphatase type IVA, member 3 (PTP4A3), and the transforming growth factor beta 1 (TGFB1) showed a highly significant correlation between expression level and endometrial cancer overall survival (OS) and can stratify the 545 endometrial cancer patients in the TCGA cohort into a high-risk and low-risk-cohorts. Additionally, four genes within the 45 upregulated chemoresistance-associated genes are ADAMTS5, MICAL2, STAT5A, and PTP4A3 codes for proteins for which small-molecule inhibitors already exist. We identified these proteins as molecular targets for chemoresistant endometrial cancer and showed that treatment with their correspondent inhibitors effectively killed otherwise chemoresistant cells. Collectively, these findings underline the utility of matched pair of chemosensitive and chemoresistant cancer cells to identify markers for endometrial cancer risk stratification and to serve as a pharmacogenomics model for identification of alternative chemotherapy approaches for treatment of patients with recurrent disease.

The life and works of S100P - from conception to cancer

Since its discovery in 1992, the small, 10.4 kDa calcium-binding protein S100P has gained the attention of researchers from different scientific fields due to its potential roles in both healthy and neoplastic tissues. Although not ubiquitously expressed, in tissues where it is present, S100P is associated with distinct changes in cellular behaviour. In this review we have summarized the evolutionary history of S100P, its expression and involvement in implantation and human embryonic development, as well as important functions in normal tissue and cancer. Finally, we have demonstrated its pivotal role as a potential diagnostic and therapeutic target, which opens promising avenues for further fruitful research on S100P.

Serum microRNAs in clear cell carcinoma of the ovary

OBJECTIVE

To identify candidate microRNAs (miRNAs) in the serum of patients with clear cell carcinomas in monitoring disease progression.

MATERIALS AND METHODS

The sera of patients with diagnosed ovarian clear cell carcinoma were collected from 2009 to 2012. Real-time quantitative polymerase chain reaction (PCR) analysis for 270 miRNAs was performed. To offset the potential extraction bias, an equal amount of Caenorhabditis elegans cel-miR-238 was added to each serum specimen before miRNA isolation. miRNA expression was analyzed using the ΔCt method, with cel-miR-238 as controls.

RESULTS

Twenty-one patients with clear cell carcinoma were included. In the discovery phase on four pairs of pre- and postoperative sera, 18 differentially expressed miRNAs were selected from 270 miRNAs. In the validation phase on an independent set of 11 pairs of pre- and postoperative sera, 4 miRNAs (hsa-miR-130a, hsa-miR-138, hsa-miR-187, and hsa-miR-202) were confirmed to be higher in the preoperative sera. In the application phase, hsa-miR-130a remained consistent with the different time points in seven of the 10 patients during clinical follow-up periods. More importantly, in three patients, hsa-miR-130a levels were elevated in early disease recurrences before CA125 was found to be elevated.

CONCLUSION

Hsa-miR-130a may be a useful serum biomarker for detecting recurrence of ovarian clear cell cancer, and warrants further studies.

Carbonic Anhydrase XII as an Independent Prognostic Factor in Advanced Esophageal Squamous Cell Carcinoma

BACKGROUND

Although recent studies described important roles for carbonic anhydrase (CA) XII in epithelial carcinogenesis and tumor behavior, a consensus has not yet been reached regarding its clinicopathological significance in esophageal squamous cell carcinoma (ESCC). In the present study, we investigated its prognostic significance in ESCC.

MATERIALS AND METHODS

An immunohistochemical analysis was performed on 70 primary tumor samples obtained from ESCC patients who underwent esophagectomy, and the relationships between the expression of CA XII and various clinicopathological features or prognosis were analyzed.

RESULTS

Immunohistochemical staining showed that CA XII was primarily found in the cell membranes of carcinoma cells. Although the expression of CA XII was related to the pT category, it had no prognostic impact. We then examined the expression of CA XII according to the pT category. In pT2-3 ESCC, the 3-year survival rate of patients with the high grade expression of CA XII (29.1 %) was significantly lower than that of patients with the low grade expression of CA XII (70.3 %). Furthermore, a multivariate analysis demonstrated that the expression of CA XII was one of the most important independent prognostic factors following radical esophagectomy in pT2-3 ESCC.

CONCLUSION

These results suggest that the expression of CA XII may be a valuable prognostic factor for patients with advanced ESCC. The results of the present study provide an insight into the role of CA XII as a biomarker in ESCC.

Gene expression profiling reveals activation of the FA/BRCA pathway in advanced squamous cervical cancer with intrinsic resistance and therapy failure

Background

Advanced squamous cervical cancer, one of the most commonly diagnosed cancers in women, still remains a major problem in oncology due to treatment failure and distant metastasis. Antitumor therapy failure is due to both intrinsic and acquired resistance; intrinsic resistance is often decisive for treatment response. In this study, we investigated the specific pathways and molecules responsible for baseline therapy failure in locally advanced squamous cervical cancer.

Methods

Twenty-one patients with locally advanced squamous cell carcinoma were enrolled in this study. Primary biopsies harvested prior to therapy were analyzed for whole human gene expression (Agilent) based on the patient’s 6 months clinical response. Ingenuity Pathway Analysis was used to investigate the altered molecular function and canonical pathways between the responding and non-responding patients. The microarray results were validated by qRT-PCR and immunohistochemistry. An additional set of 24 formalin-fixed paraffin-embedded cervical cancer samples was used for independent validation of the proteins of interest.

Results

A 2859-gene signature was identified to distinguish between responder and non-responder patients. ‘DNA Replication, Recombination and Repair’ represented one of the most important mechanisms activated in non-responsive cervical tumors, and the ‘Role of BRCA1 in DNA Damage Response’ was predicted to be the most significantly altered canonical pathway involved in intrinsic resistance (p = 1.86E-04, ratio = 0.262). Immunohistological staining confirmed increased expression of BRCA1, BRIP1, FANCD2 and RAD51 in non-responsive compared with responsive advanced squamous cervical cancer, both in the initial set of 21 cervical cancer samples and the second set of 24 samples.

Conclusions

Our findings suggest that FA/BRCA pathway plays an important role in treatment failure in advanced cervical cancer. The assessment of FANCD2, RAD51, BRCA1 and BRIP1 nuclear proteins could provide important information about the patients at risk for treatment failure.

Carbonic anhydrase XII expression is associated with histologic grade of cervical cancer and superior radiotherapy outcome

Background

To investigate whether expression of carbonic anhydrase XII (CA12) is associated with histologic grade of the tumors and radiotherapy outcomes of the patients with invasive cervical cancer.

Methods

CA12 expression was examined by immunohistochemical stains in cervical cancer tissues from 183 radiotherapy patients. Histological grading was classified as well (WD), moderately (MD) or poorly differentiated (PD). Oligonucleotide microarray experiment was performed using seven cervical cancer samples to examine differentially expressed genes between WD and PD cervical cancers. The association between CA12 and histological grade was analyzed by chi-square test. CA12 and histological grades were analyzed individually and as combined CA12 and histologic grade categories for effects on survival outcome.

Results

Immunohistochemical expression of CA12 was highly associated with the histologic grade of cervical cancer. Lack of CA12 expression was associated with PD histology, with an odds ratio of 3.9 (P = 0.01). Microarray analysis showed a fourfold reduction in CA12 gene expression in PD tumors. CA12 expression was marginally associated with superior disease-free survival. Application of the new combined categories resulted in further discrimination of the prognosis of patients with moderate and poorly differentiated tumor grade.

Conclusions

Our study indicates that CA12 may be used as a novel prognostic marker in combination with histologic grade of the tumors.

Molecular characterization of early adenocarcinoma of the uterine cervix by oligonucleotide microarray

PURPOSE

In an attempt to understand the molecular characterization for the early adenocarcinoma of the uterine cervix, an analysis of gene expression profiles obtained from early adenocarcinoma of the uterine cervix was performed to find those genes most aberrantly expressed.

METHODS AND MATERIALS

Total RNA was prepared from 32 samples of early adenocarcinoma of the uterine cervix and 32 paired normal cervix tissues, and hybridized to cancer-associated oligonucleotide microarrays with probe sets complementary to about 1,426 transcripts.

RESULTS

Supervised analysis of gene expression data identified 13 genes that exhibited >2-fold upregulation and 27 genes >2-fold downregulation, respectively, in early adenocarcinoma of the uterine cervix compared to normal cervix. Unsupervised hierarchical clustering of the expression data readily distinguished early adenocarcinoma of the uterine cervix from normal cervix. Two genes (karyopherin alpha 2 and proliferating cell nuclear antigen) were selected randomly for real-time reverse transcription polymerase chain reaction analysis. Both genes were expressed significantly higher in early adenocarcinoma of the uterine cervix than in normal cervix, with p = 0.0003 and <0.0001, respectively. These results were compatible with the microarray data.

CONCLUSIONS

This study has revealed several genes that may be highly attractive candidate molecular markers/targets for early adenocarcinoma of the uterine cervix.

Microarray analysis of gene expression of cancer to guide the use of chemotherapeutics

The beauty of microarray analysis of gene expression (MAGE) is that it can be used to discover some genes that were previously thought to be unrelated to a physiologic or pathologic event. During the period from 1999 to 2007, applications of MAGE in cancer investigation have shifted from molecular profiling, identifying previously undiscovered cancer types, predicting outcomes of cancer patients, revealing metastasis signatures of solid tumors, to guiding the use of therapeutics. The roles of cancer genomic signatures have evolved through three phases. In the first phase, genomic signatures were described in stored cancer specimens and dubbed as molecular portraits of cancer. When gene expression profiles were carefully correlated with sufficient clinical information of cancer patients, new subgroups of cancers with distinct outcomes were revealed. In studies of the second phase, validation of cancer signatures was emphasized and commonly performed with independent groups of cancer specimens or independent data set. In the third phase, cancer genomic signatures have been further expanded beyond depicting the molecular portrait of cancer to predicting patient outcomes and guiding the use of cancer therapeutics. Cancer genomic signatures have become an essential part of a new generation of cancer clinical trials. It is advocated that, in future clinical trials of cancer therapy, the cancer specimens of each participant should be tested for currently available predictor genomic signatures, so that the most effective treatment with the least adverse effects for each patient can be identified. Then, participants can be triaged to an appropriate study group.