Profiling Of Cancer Cell Lines Research Articles

Cytosine methylation profiling of cancer cell lines

DNA-methylation changes in human cancer are complex and vary between the different types of cancer. Capturing this epigenetic variability in an atlas of DNA-methylation changes will be beneficial for basic research as well as translational medicine. Hypothesis-free approaches that interrogate methylation patterns genome-wide have already generated promising results. However, these methods are still limited by their quantitative accuracy and the number of CpG sites that can be assessed individually. Here, we use a unique approach to measure quantitative methylation patterns in a set of >400 candidate genes. In this high-resolution study, we employed a cell-line model consisting of 59 cancer cell lines provided by the National Cancer Institute and six healthy control tissues for discovery of methylation differences in cancer-related genes. To assess the effect of cell culturing, we validated the results from colon cancer cell lines by using clinical colon cancer specimens. Our results show that a large proportion of genes (78 of 400 genes) are epigenetically altered in cancer. Although most genes show methylation changes in only one tumor type (35 genes), we also found a set of genes that changed in many different forms of cancer (seven genes). This dataset can easily be expanded to develop a more comprehensive and ultimately complete map of quantitative methylation changes. Our methylation data also provide an ideal starting point for further translational research where the results can be combined with existing large-scale datasets to develop an approach that integrates epigenetic, transcriptional, and mutational findings.

Silencing expression of UO-44 (CUZD1) using small interfering RNA sensitizes human ovarian cancer cells to cisplatin in vitro

Ovarian cancer is currently the second leading cause of gynecological malignancy and cisplatin or cisplatin-based regimens have been the standard of care for the treatment of advance epithelial ovarian cancers. However, the efficacy of cisplatin treatment is often limited by the development of drug resistance either through the inhibition of apoptotic genes or activation of antiapoptotic genes. We have previously reported the overexpression of human UO-44 (HuUO-44) in ovarian cancers and the HuUO-44 antisera markedly inhibited NIH-OVCAR3 ovarian cancer cell attachment and proliferation (Oncogene 23: 5707-5718, 2004). In the present study, we observed through the cancer cell line profiling array that the expression of HuUO-44 was suppressed in the ovarian cancer cell line (SKOV-3) after treatment with several chemotherapeutic drugs. Similarly, this suppression in HuUO-44 expression was also correlated to the cisplatin sensitivity in two other ovarian cancer cell lines NIH-OVCAR3 and OV-90 in a dose-dependent manner. To elucidate the function of HuUO-44 in cisplatin chemoresistance in ovarian cancer cell, small interfering RNAs (siRNAs) were employed to mediate HuUO-44 silencing in ovarian cancer cell line, NIH-OVCAR3. HuUO-44 RNA interference (RNAi) resulted in the inhibition of cell growth and proliferation. Importantly, HuUO-44 RNAi significantly increased sensitivity of NIH-OVCAR3 to cytotoxic stress induced by cisplatin (P<0.01). Strikingly, we have also demonstrated that overexpression of HuUO-44 significantly conferred cisplatin resistance in NIH-OVCAR3 cells (P<0.05). Taken together, UO-44 is involved in conferring cisplatin resistance; the described HuUO-44-specific siRNA oligonucleotides that can potently silence HuUO-44 gene expression may prove to be valuable pretreatment targets for antitumor therapy or other pathological conditions that involves aberrant HuUO-44 expression.

Cytosine Β-D Arabino-Furanoside (Ara-C) and CPT-11 inhibit cell proliferation in human colorectal cancer with microsatellite instability

2061 Background: Recent studies suggest 5-Fluorouracil-based adjuvant chemotherapy does not improve survival in colorectal cancer (CRC) patients with microsatellite instability (MSI) (NEJM, 349 July: 247–257, 2003). We have reported decreased expression of p12DOC-1 is associated with increased proliferation and apoptosis arrest in human CRC with MSI (Oncogene, 22: 6304–10, 2003). The purpose of this study was to measure differential expression of p12DOC-1 using a Cancer Cell Line Profiling (CCLP) Array (Clontech) and to assess the efficacy of CPT-11 and oxaliplatin, in human MSI CRC cell lines. Methods: A CCLP array containing 702 complex cDNA samples from 26 different human cancer cell lines was treated with a range of chemotherapeutic agents. The array was hybridized with a p32-dCTP labeled p12DOC-1 probe. Array results were confirmed using real-time RT-PCR. In addition, the toxicity of CPT-11 and oxaliplatin (neither agent tested on array) against CRC cell lines, RKO (MSI) and SW480 (microsatellite sta...

Cytosine Β-D Arabino-Furanoside (Ara-C) and CPT-11 inhibit cell proliferation in human colorectal cancer with microsatellite instability

2061 Background: Recent studies suggest 5-Fluorouracil-based adjuvant chemotherapy does not improve survival in colorectal cancer (CRC) patients with microsatellite instability (MSI) (NEJM, 349 July: 247–257, 2003). We have reported decreased expression of p12DOC-1 is associated with increased proliferation and apoptosis arrest in human CRC with MSI (Oncogene, 22: 6304–10, 2003). The purpose of this study was to measure differential expression of p12DOC-1 using a Cancer Cell Line Profiling (CCLP) Array (Clontech) and to assess the efficacy of CPT-11 and oxaliplatin, in human MSI CRC cell lines. Methods: A CCLP array containing 702 complex cDNA samples from 26 different human cancer cell lines was treated with a range of chemotherapeutic agents. The array was hybridized with a p32-dCTP labeled p12DOC-1 probe. Array results were confirmed using real-time RT-PCR. In addition, the toxicity of CPT-11 and oxaliplatin (neither agent tested on array) against CRC cell lines, RKO (MSI) and SW480 (microsatellite stable), was measured pre and post transfection with pcDNA3-p12DOC-1. Cell survival was assessed by MTT assay and expressed as IC50 values (50% inhibitory concentration). Results: Ara-C increased p12DOC-1 expression in 2 of 3 MSI CRC cell lines by CCLP array and was confirmed by real-time RT-PCR. Significantly decreased S phase and increased apoptosis was also observed. RT-PCR confirmed an 8-fold increase in p12DOC-1 expression in MSI CRC cell lines after transfection with pcDNA3-p12DOC-1. IC50 values for CPT-11 were significantly higher in all cell lines with increased p12DOC-1 expression (mean IC50= 37 μM), compared to the RKO wild type control (minimal DOC-1 expression) (IC50 =1 μM) (p< 0.05). No differential IC50 values were observed for oxaliplatin. Conclusions: Ara-C induces p12DOC-1 expression, inhibits cell proliferation and increases apoptosis in MSI CRC. In addition, MSI CRC is extremely sensitive to CPT-11. These results suggest that differential gene expression analysis may assist selection of optimal chemotherapeutic agents specifically for the treatment of 5FU resistant MSI CRC. No significant financial relationships to disclose.