Ligand-directed surface profiling of human cancer cells with combinatorial peptide libraries

A collection of 60 cell lines derived from human tumors (NCI-60) has been widely explored as a tool for anticancer drug discovery. Here, we profiled the cell surface of the NCI-60 by high-throughput screening of a phage-displayed random peptide library and classified the cell lines according to the binding selectivity of 26,031 recovered tripeptide motifs. By analyzing selected cell-homing peptide motifs and their NCI-60 recognition patterns, we established that some of these motifs (a) are similar to domains of human proteins known as ligands for tumor cell receptors and (b) segregate among the NCI-60 in a pattern correlating with expression profiles of the corresponding receptors. We biochemically validated some of the motifs as mimic peptides of native ligands for the epidermal growth factor receptor. Our results indicate that ligand-directed profiling of tumor cell lines can select functional peptides from combinatorial libraries based on the expression of tumor cell surface molecules, which in turn could be exploited as "druggable" receptors in specific types of cancer.     

MicroRNA profiling in human medulloblastoma

Medulloblastoma is an aggressive brain malignancy with high incidence in childhood. Current treatment approaches have limited efficacy and severe side effects. Therefore, new risk-adapted therapeutic strategies based on molecular classification are required. MicroRNA expression analysis has emerged as a powerful tool to identify candidate molecules playing an important role in a large number of malignancies. However, no data are yet available on human primary medulloblastomas. A high throughput microRNA expression profiles was performed in human primary medulloblastoma specimens to investigate microRNA involvement in medulloblastoma carcinogenesis. We identified specific microRNA expression patterns which distinguish medulloblastoma differing in histotypes (anaplastic, classic and desmoplastic), in molecular features (ErbB2 or c-Myc overexpressing tumors) and in disease-risk stratification. MicroRNAs expression profile clearly differentiates medulloblastoma from either adult or fetal normal cerebellar tissues. Only a few microRNAs displayed upregulated expression, while most of them were downregulated in tumor samples, suggesting a tumor growth-inhibitory function. This property has been addressed for miR-9 and miR-125a, whose rescued expression promoted medulloblastoma cell growth arrest and apoptosis while targeting the proproliferative truncated TrkC isoform. In conclusion, misregulated microRNA expression profiles characterize human medulloblastomas, and may provide potential targets for novel therapeutic strategies.     

MicroRNA expression profile of gastrointestinal stromal tumors is distinguished by 14q loss and anatomic site

MicroRNAs are known to regulate gene expression. Although unique microRNA expression profiles have been reported in several tumors, little is known about microRNA expression profiles in GISTs. To evaluate the relationship between microRNA expression and clinicopathologic findings of GISTs, we analyzed the microRNA expression profiles of GISTs. We used fresh frozen tissues from 20 GISTs and analyzed KIT and PDGFRA mutations and chromosomal loss status. MicroRNA expression was analyzed using a microRNA chip containing 470 microRNAs. Using unsupervised hierarchical clustering analysis, we found four distinct microRNA expression patterns in our 20 GISTs. Six GISTs that did not have 14q loss formed a separate cluster. In the 14 GISTs with 14q loss, 5 small bowel GISTs formed a separate cluster and the remaining 9 GISTs could be divided into two groups according to frequent chromosomal losses and tumor risk. We found 73 microRNAs that were significantly down‐regulated in the GISTs with 14q loss; 38 of these microRNAs are encoded on 14q. We also found many microRNAs that were down‐regulated in small bowel and high‐risk group GISTs. Most of the microRNAs down‐regulated in the high‐risk group and small bowel GISTs are known to be involved in tumor progression, specifically by stimulating mitogen‐activated protein kinase (MAPK) and the cell cycle. The microRNA expression patterns of GISTs are closely related to the status of 14q loss, anatomic site, and tumor risk. These findings suggest that microRNA expression patterns can differentiate several subsets of GISTs.     

Alterations of microRNAs contribute to colon carcinogenesis

MicroRNAs are being evaluated as biomarkers and therapeutic targets for colon cancer. MicroRNAs have a functional role in the initiation and progression of colon cancer. Altered microRNA expression is found in tumors and their expression patterns may serve as useful cancer biomarkers. Polymorphisms in microRNAs or microRNA binding sites may modify the risk of developing cancer. As we continue to improve our understanding of the role for microRNAs in the initiation and progression of cancer, one goal is to gain insights that will allow for the development of microRNAs as biomarkers and therapeutic targets for cancer. This review provides a current understanding of the connection between microRNAs and colon cancer. We will cover evidence that global microRNA expression patterns are altered in colon tumors, that specific microRNAs have a functional role in colon carcinogenesis, that polymorphisms in microRNAs may be associated with risk of colon cancer, and the potential for using circulating microRNAs as a noninvasive biomarker for the detection of cancer.     

Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines

The concept of tumor stem cells (TSCs) provides a new paradigm for understanding tumor biology, although it remains unclear whether TSCs will prove to be a more robust model than traditional cancer cell lines. We demonstrate marked phenotypic and genotypic differences between primary human tumor-derived TSCs and their matched glioma cell lines. Unlike the matched, traditionally grown tumor cell lines, TSCs derived directly from primary glioblastomas harbor extensive similarities to normal neural stem cells and recapitulate the genotype, gene expression patterns, and in vivo biology of human glioblastomas. These findings suggest that TSCs may be a more reliable model than many commonly utilized cancer cell lines for understanding the biology of primary human tumors.     

Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen

The 60 cell lines of the National Cancer Institute Anticancer Drug Screen (NCI-60) constitute the most extensively characterized in vitro cancer cell model. They have been tested for sensitivity to more than 100,000 potential chemotherapy agents and have been profiled extensively at the DNA, RNA, protein, functional, and pharmacologic levels. We have used the NCI-60 cell lines and three additional lines to develop a database of responses of cancer cells to ionizing radiation. We compared clonogenic survival, apoptosis, and gene expression response by microarray. Although several studies have profiled relative basal gene expression in the NCI-60, this is the first comparison of large-scale gene expression changes in response to genotoxic stress. Twenty-two genes were differentially regulated in cells with low survival after 2-Gy gamma-rays; 14 genes identified lines more sensitive to 8 Gy. Unlike reported basal gene expression patterns, changes in expression in response to radiation showed little tissue-of-origin effect, except for differentiating the lymphoblastoid cell lines from other cell types. Basal expression patterns, however, discriminated well between radiosensitive and more resistant lines, possibly being more informative than radiation response signatures. The most striking patterns in the radiation data were a set of genes up-regulated preferentially in the p53 wild-type lines and a set of cell cycle regulatory genes down-regulated across the entire NCI-60 panel. The response of those genes to gamma-rays seems to be unaffected by the myriad of genetic differences across this diverse cell set; it represents the most penetrant gene expression response to ionizing radiation yet observed.     

Emerging functions of microRNAs in glioblastoma

Distinct patterns of microRNA expression have been observed in glioblastomas. The functional significance of some of these microRNAs is beginning to emerge. This data indicates that microRNAs play roles in multiple hallmark biological characteristics of glioblastoma, including cell proliferation, invasion, glioma stem cell behavior, and angiogenesis. Research in this area is quickly gathering pace and is illuminating important aspects of the disease that may ultimately lead to novel therapeutic interventions, as well as diagnostic and prognostic tools for brain tumors.     

Human tumor microRNA signatures derived from large-scale oligonucleotide microarray datasets

The expression profiles of microRNAs (miRNAs) are associated with the initiation and progression of human tumors. DNA microarrays are widely used to explore the expression patterns of miRNAs. Because of the limited sample size and experimental expense, the statistical power of individual research projects is not sufficient to yield a robust conclusion. However, collected microarray datasets of expression profiles provide opportunities to compile the information of individual studies. Our study carried out a comprehensive meta-analysis of miRNA expression microarray datasets from 28 published tumor studies; it comprises 33 comparisons and nearly 4,000 tumor and corresponding nontumorous samples. This work reports 52 miRNAs as common signatures that are dysregulated in tumors. In addition to the commonly altered miRNAs, five solid cancers displayed specific tissue patterns of altered miRNAs as well. The meta-analysis also revealed some novel tumor-related miRNAs such as hsa-miR-144, hsa-miR-130b, hsa-miR-132, hsa-miR-154, hsa-miR-192 and hsa-miR-345. We further validated the expression pattern of hsa-miR-154 in human hepatocellular carcinoma by RT-PCR. Restoration of intracellular miR-154 inhibited tumor cell malignance and the G(1)/S transition in cancer cells. Both bioinformatic prediction and western blotting demonstrated that miR-154 could target CCND2. In addition, expression patterns of miR-154 were inversely correlated with those of CCND2 in hepatocellular carcinoma. Overall, this study used a large-scale data analysis to identify a qualified list of miRNAs that are consistently changed in tumors, which could lead to a better understanding of human tumor etiology.     

Systematic analysis of microRNA involved in resistance of the MCF-7 human breast cancer cell to doxorubicin

Multidrug resistance remains a major clinical obstacle to successful treatment of breast cancer and leads to poor prognosis for the patients. Recently studies have shown that microRNAs play an important role in breast cancer cell resistance to chemotherapeutic agents. In this study, microRNA expression profiles of MCF-7/AdrVp and MCF-7 were analyzed using microarray and the results were confirmed by real-time RT-polymerase chain reaction. Gene Ontology (GO) and pathways mapping tools were employed to analyse systemically the biological processes and signaling pathways affected by differential expression microRNAs. Here, we showed that 181 human microRNAs were differentially expressed between two cell lines. Compared to MCF-7 cells, there were 16 microRNAs down-regulated and 165 microRNAs up-regulated in MCF-7/AdrVp. Western blot confirmed the correlation between specific microRNA expression and corresponding changes in protein levels of their targets, specifically those that have a documented role in cancer drug resistance. Furthermore, we validated that signaling pathway highlighted in the study was involved in drug resistance. These results indicated that breast cancer cell resistant to chemotherapy was associated with a group of microRNAs. GO and pathway mapping are valid and effective approach to analyse the function of microRNAs and the results could be a guideline for further investigation.     

Genetic and epigenetic silencing of microRNA-203 enhances ABL1 and BCR-ABL1 oncogene expression

The mammalian genome contains several hundred microRNAs that regulate gene expression through modulation of target mRNAs. Here, we report a fragile chromosomal region lost in specific hematopoietic malignancies. This 7 Mb region encodes about 12% of all genomic microRNAs, including miR-203. This microRNA is additionally hypermethylated in several hematopoietic tumors, including chronic myelogenous leukemias and some acute lymphoblastic leukemias. A putative miR-203 target, ABL1, is specifically activated in these hematopoietic malignancies in some cases as a BCR-ABL1 fusion protein (Philadelphia chromosome). Re-expression of miR-203 reduces ABL1 and BCR-ABL1 fusion protein levels and inhibits tumor cell proliferation in an ABL1-dependent manner. Thus, miR-203 functions as a tumor suppressor, and re-expression of this microRNA might have therapeutic benefits in specific hematopoietic malignancies.     

MicroRNAs in cancer treatment and prognosis

Disturbances in microRNA expression by epigenetic alterations and mutations may promote not only tumorigenesis but also tumor aggressiveness, invasion, metastasis, and resistance to chemotherapy and radiotherapy. Several studies have profiled microRNA expression in normal and tumorigenic tissues, demonstrating a unique microRNA signature, which can be used as a marker for cancer diagnosis and prognosis. This review discusses the importance of microRNAs as regulatory biomolecules involved in cancer, focusing on microRNAs related to cancer invasion, metastasis, epigenetic alterations, chemoresistance, and radioresistance. The identification of both differentially expressed microRNAs in tumors and their target genes provides new tools for gene therapy; the re-expression of microRNAs silenced by cancer development or the silencing of oncogenic microRNAs can be effective in the blockade of cancer-related cell proliferation.