Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer

A full-genomic sequence-verified protein-coding gene collection for Francisella tularensis

The rapid development of new technologies for the high throughput (HT) study of proteins has increased the demand for comprehensive plasmid clone resources that support protein expression. These clones must be full-length, sequence-verified and in a flexible format. The generation of these resources requires automated pipelines supported by software management systems. Although the availability of clone resources is growing, current collections are either not complete or not fully sequence-verified. We report an automated pipeline, supported by several software applications that enabled the construction of the first comprehensive sequence-verified plasmid clone resource for more than 96% of protein coding sequences of the genome of F. tularensis, a highly virulent human pathogen and the causative agent of tularemia. This clone resource was applied to a HT protein purification pipeline successfully producing recombinant proteins for 72% of the genes. These methods and resources represent significant technological steps towards exploiting the genomic information of F. tularensis in discovery applications.

Aloe-emodin metabolites protected N-methyl-d-aspartate-treated retinal ganglion cells by Cu-Zn superoxide dismutase

A high concentration of glutamate in the eyes not only activates N-methyl-D-aspartate (NMDA) receptors, but also is toxic to the retina ganglion cells (RGCs) in glaucomatous patients. Our previous study had found that aloe-emodin sulfates/glucuronides metabolites, an anthraquinone polyphenol, exerted a neuroprotective activity upon RGCs. In order to understand the mechanisms involved in this neuroprotective effect, this study aimed to determine the expressions of RNAs and proteins in various treatments. The proteins expressed in the control group, NMDA-treated group, and aloe-emodin metabolites-cotreated group were separated by two-dimensional gel electrophoresis (2-DE). Protein spots were excised from 2-DE and analyzed by nano-LC-MS/MS (nano-liquid chromatography with mass spectrometry; tandem MS). Quantitative polymerase chain reaction (Q-PCR) was used to investigate the RNA related to these proteins. There were 84 spots with significant differences in various treatments. Among the 84 spots, we identified 9 spots whose functions were closely related to regulate the apoptosis of cells. The results of Q-PCR were not completely unanimous with those of 2-DE. Our results suggested that aloe-emodin metabolites decreased NMDA-induced apoptosis of RGCs by preserving, and inducing, some proteins related to the antioxidation and regulation of cells' energy. Both the level of RNA and protein of superoxide dismutase (Cu-Zn) were significantly elevated after aloe-emodin metabolites were added. The mechanisms of neuroprotection are complicated, and involve not only the transcription and stability of mRNA, but also post-translation protein modifications, degradation, and protein-protein interaction.

ETS transcription factors in endocrine systems

E26 transformation-specific (ETS) transcription factors have become increasingly recognized as key regulators of differentiation, hormone responses and tumorigenesis in endocrine organs and target tissues. The ETS family is highly diverse, consisting of both transcription activators and repressors that mediate growth factor signaling and regulate gene expression through combinatorial interactions with multiple protein partners on composite DNA elements. ETS proteins have a role in the endocrine system in establishing pituitary-specific gene expression, mammary gland development and cancers of the breast, prostate and reproductive organs.

Strategies for plasma proteomic profiling of cancers

Despite a voluminous literature on potential protein biomarkers and a compelling need for diagnostic tests based on biomarkers to detect cancers at much earlier, more treatable stages, progress has been limited. New methods and new instruments for analysis of differences in gene expression, gene methylation, and proteomics are being employed to try to accelerate the discovery phase. Given the heterogeneity of tumor mechanisms and the limitations of analytical methods, it is likely that a variety of strategies will be needed and will be complementary. That is the basis of this review of proteomic approaches. This article adopts a systems biology view, starting with mRNA transcripts in tumors and cultured tumor cells to detect mRNA overexpression, some of which will be correlated with protein overexpression. Some of those proteins may be secreted or released into proximal biofluids and plasma. Detection of low-abundance tumor proteins in the complex and dynamic mixture that is plasma requires combinations of increasingly powerful technologies. The biological amplification of protein signals through the immune system offers autoantibodies as potential biomarkers. Higher abundance proteins, including acute-phase reactants, may have practical value, especially if the proteins are modified as part of the cancer processes. Low molecular weight proteins, fragments, and peptides may offer complementary biomarkers. Promising biomarker candidates must be confirmed in independent studies. Then they must be submitted to higher-throughput methods practical for large-scale validation studies and, hopefully, for clinical and epidemiological applications. Standardized operating procedures for specimen handling, design and use of various reference standards, care to avoid bias and confounding, and guidelines for reporting findings and contributing datasets should enhance the prospects for predictive proteomic profiling of people at risk for cancers.

PlasmID: a centralized repository for plasmid clone information and distribution

The Plasmid Information Database (PlasmID; ) was developed as a community-based resource portal to facilitate search and request of plasmid clones shared with the Dana-Farber/Harvard Cancer Center (DF/HCC) DNA Resource Core. PlasmID serves as a central data repository and enables researchers to search the collection online using common gene names and identifiers, keywords, vector features, author names and PubMed IDs. As of October 2006, the repository contains >46 000 plasmids in 98 different vectors, including cloned cDNA and genomic fragments from 26 different species. Moreover, the clones include plasmid vectors useful for routine and cutting-edge techniques; functionally related sets of human cDNA clones; and genome-scale gene collections for Saccharomyces cerevisiae, Pseudomonas aeruginosa, Yersinia pestis, Francisella tularensis, Bacillus anthracis and Vibrio cholerae. Information about the plasmids has been fully annotated in adherence with a high-quality standard, and clone samples are stored as glycerol stocks in a state-of-the-art automated −80°C freezer storage system. Clone replication and distribution is highly automated to minimize human error. Infor-mation about vectors and plasmid clones, including downloadable maps and sequence data, is freely available online. Researchers interested in requesting clone samples or sharing their own plasmids with the repository can visit the PlasmID website for more information.

Transforming properties of YAP, a candidate oncogene on the chromosome 11q22 amplicon

In a screen for gene copy-number changes in mouse mammary tumors, we identified a tumor with a small 350-kb amplicon from a region that is syntenic to a much larger locus amplified in human cancers at chromosome 11q22. The mouse amplicon contains only one known gene, Yap, encoding the mammalian ortholog of Drosophila Yorkie (Yki), a downstream effector of the Hippo(Hpo)-Salvador(Sav)-Warts(Wts) signaling cascade, recently identified in flies as a critical regulator of cellular proliferation and apoptosis. In nontransformed mammary epithelial cells, overexpression of human YAP induces epithelial-to-mesenchymal transition, suppression of apoptosis, growth factor-independent proliferation, and anchorage-independent growth in soft agar. Together, these observations point to a potential oncogenic role for YAP in 11q22-amplified human cancers, and they suggest that this highly conserved signaling pathway identified in Drosophila regulates both cellular proliferation and apoptosis in mammalian epithelial cells.