The 3-phosphorylated inositol lipids fulfill roles as second messengers by interacting with the lipid binding domains of a variety of cellular proteins. Such interactions can affect the subcellular localization and aggregation of target proteins, and through allosteric effects, their activity. Generation of 3-phosphoinositides has been documented to influence diverse cellular pathways and hence alter a spectrum of fundamental cellular activities. This review is focused on the 3-phosphoinositide lipids, the synthesis of which is acutely triggered by extracellular stimuli, the enzymes responsible for their synthesis and metabolism, and their cell biological roles. Much knowledge has recently been gained through structural insights into the lipid kinases, their interaction with inhibitors, and the way their 3-phosphoinositide products interact with protein targets. This field is now moving toward a genetic dissection of 3-phosphoinositide action in a variety of model organisms. Such approaches will reveal the true role of the 3-phosphoinositides at the organismal level in health and disease.

The phosphoinositide 3-kinase (PI3K) family of enzymes is recruited upon growth factor receptor activation and produces 3' phosphoinositide lipids. The lipid products of PI3K act as second messengers by binding to and activating diverse cellular target proteins. These events constitute the start of a complex signaling cascade, which ultimately results in the mediation of cellular activities such as proliferation, differentiation, chemotaxis, survival, trafficking, and glucose homeostasis. Therefore, PI3Ks play a central role in many cellular functions. The factors that determine which cellular function is mediated are complex and may be partly attributed to the diversity that exists at each level of the PI3K signaling cascade, such as the type of stimulus, the isoform of PI3K, or the nature of the second messenger lipids. Numerous studies have helped to elucidate some of the key factors that determine cell fate in the context of PI3K signaling. For example, the past two years has seen the publication of many transgenic and knockout mouse studies where either PI3K or its signaling components are deregulated. These models have helped to build a picture of the role of PI3K in physiology and indeed there have been a number of surprises. This review uses such models as a framework to build a profile of PI3K function within both the cell and the organism and focuses, in particular, on the role of PI3K in cell regulation, immunity, and development. The evidence for the role of deregulated PI3K signaling in diseases such as cancer and diabetes is reviewed.

The PI3Ks (phosphatidylinositol 3-kinases) regulate cellular signalling networks that are involved in processes linked to the survival, growth, proliferation, metabolism and specialized differentiated functions of cells. The subversion of this network is common in cancer and has also been linked to disorders of inflammation. The elucidation of the physiological function of PI3K has come from pharmacological studies, which use the enzyme inhibitors Wortmannin and LY294002, and from PI3K genetic knockout models of the effects of loss of PI3K function. Several reports have shown that LY294002 is not exclusively selective for the PI3Ks, and could in fact act on other lipid kinases and additional apparently unrelated proteins. Since this inhibitor still remains a drug of choice in numerous PI3K studies (over 500 in the last year), it is important to establish the precise specificity of this compound. We report here the use of a chemical proteomic strategy in which an analogue of LY294002, PI828, was immobilized onto epoxy-activated Sepharose beads. This affinity material was then used as a bait to fish-out potential protein targets from cellular extracts. Proteins with high affinity for immobilized PI828 were separated by one-dimensional gel electrophoresis and identified by liquid chromatography-tandem MS. The present study reveals that LY294002 not only binds to class I PI3Ks and other PI3K-related kinases, but also to novel targets seemingly unrelated to the PI3K family.

The technique of fluorescent two-dimensional (2D) difference gel electrophoresis for differential protein expression analysis has been evaluated using a model breast cancer cell system of ErbB-2 overexpression. Labeling of paired cell lysate samples with N-hydroxy succinimidyl ester-derivatives of fluorescent Cy3 and Cy5 dyes for separation on the same 2D gel enabled quantitative, sensitive, and reproducible differential expression analysis of the cell lines. SyproRuby staining was shown to be a highly sensitive and 2D difference gel electrophoresis-compatible method for post-electrophoretic visualization of proteins, which could then be picked and identified by matrixassisted laser-desorption ionization mass spectroscopy. Indeed, from these experiments, we have identified multiple proteins that are likely to be involved in ErbB-2-mediated transformation. A triple dye labeling methodology was used to identify proteins differentially expressed in the cell system over a time course of growth factor stimulation. A Cy2-labeled pool of samples was used as a standard with all Cy3-and Cy5-labeled sample pairs to facilitate cross-gel quantitative analysis. DeCyder (Amersham Biosciences, Inc.) software was used to distinguish clear statistical differences in protein expression over time and between the cell lines. Molecular & Cellular Proteomics 1:91-98, 2002.The ability to determine statistically significant alterations in protein expression that correlate with disease or occur consequent to experimentally induced changes in cells is fundamental to the exploitation of proteomics. Previous studies from our laboratory have used two-dimensional (2D) 1 gel analysis of immunomagnetic affinity-sorted primary human breast cells to establish the protein expression profiles of luminal and myoepithelial cells (1). These differential expression studies were carried out using replicate 2D gels of each sample and post-staining with a fluorescent protein dye. The subsequent detailed curation and correlation of images was used to derive data sets for statistical analysis. This approach was attractive, because the fluorescent protein stain has a wide linear range of detection, thus giving improved quantification of both high and low abundance proteins. However, in these experiments, many pairs of gels were required to establish statistically significant differences in protein expression as each gel contains inherent experimental variations that limit image superimposition.The introduction of fluorescent 2D differential gel electrophoresis (DIGE) by Unlu et al. (2) has now made it possible to detect and quantitate differences between experimental pairs of samples resolved on the same 2D gel. The basis of the technique is the use of two mass-and charge-matched Nhydroxy succinimidyl ester derivatives of the fluorescent cyanine dyes Cy3 and Cy5, which possess distinct excitation and emission spectra. These are used to differentially label lysine residues of two protein samples for comparative analysis of the mixed sample on one gel. The ab...

The nontransmembrane protein tyrosine phosphatase SHP-2 plays a critical role in growth factor and cytokine signaling pathways. Previous studies revealed that a fraction of SHP-2 moves to focal contacts upon integrin engagement and that SHP-2 binds to SHP substrate 1 (SHPS- Complex processes such as cell growth, differentiation, and migration require the integration of multiple types of extracellular signals, including those delivered by growth factors, cytokines, and hormones (soluble signals), and solid-state signals, transmitted by cell-cell and cell-extracellular matrix (ECM) interactions. Most of these signaling pathways involve changes in cellular tyrosyl phosphorylation. Tyrosyl phosphorylation is regulated by protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). Although many PTKs are implicated in signaling pathways for both soluble and solid-state signals, the roles of specific PTPs are less well defined.1Multiple reverse-genetic studies suggest that the nontransmembrane PTP SHP-2 is a required positive (i.e., signalenhancing) component of growth factor and cytokine signal transduction pathways (for reviews, see references 35, 56, and 63). Consistent with these studies, fibroblasts from mice containing a deletion of SHP-2 exon 3 (hereafter referred to as SHP-2 mutant mice), which express low levels of a defective SHP-2 protein that lacks its N-terminal SH2 domain (48), exhibit impaired mitogen-activated protein kinase (MAPK) activation in response to fibroblast growth factor (FGF), epidermal growth factor, and insulin-like growth factor I (48, 55). SHP-2 functions similarly in lower organisms. Dominant-negative SHP-2 blocks FGF-induced mesoderm induction in Xenopus ectodermal explants and completion of gastrulation in early embryos, leading to severe tail truncations (38, 57). Likewise, corkscrew (csw), the Drosophila SHP-2 homolog (39, 40), is required for multiple receptor tyrosine kinase (RTK) pathways involved in early development (e.g., Torso, Sevenless, Breathless, and Drosophila EGF receptor) (1,39,40), and the recently described Caenorhabditis elegans homolog, Ptp-2, is a component of the Let-23 pathway (13).The precise mechanism by which SHP-2 orthologs function, as well as their specific target(s), has remained unclear. SHP-2 binds directly to and may dephosphorylate some growth factor and cytokine receptors (for reviews, see references 35 and 63). In other pathways, however, SHP-2 binds to distinct signaling intermediates. One class of SHP-2 binding proteins, exemplified by the Drosophila daughter of sevenless (dos) gene product, consists of an N-terminal pleckstrin homology domain and multiple proline-rich stretches and potential tyrosyl phosphorylation sites (42). Dos is essential for Sevenless signaling (15,42) and may be a direct substrate for Csw (15). Mammalian cells express several groups of molecules with overall topology similar to that of Dos (for a review, see reference 63). including insulin receptor substrate family members (for a review, see reference 64), ...

The protein tyrosine phosphatase SHP-1 is a critical regulator of macrophage biology, but its detailed mechanism of action remains largely undefined. SHP-1 associates with a 130-kDa tyrosyl-phosphorylated species (P130) in macrophages, suggesting that P130 might be an SHP-1 regulator and/or substrate. Here we show that P130 consists of two transmembrane glycoproteins, which we identify as PIR-B/p91A and the signal-regulatory protein (SIRP) family member BIT. These proteins also form separate complexes with SHP-2. BIT, but not PIR-B, is in a complex with the colony-stimulating factor 1 receptor (CSF-1R), suggesting that BIT may direct SHP-1 to the CSF-1R. BIT and PIR-B bind preferentially to substrate-trapping mutants of SHP-1 and are hyperphosphorylated in macrophages from motheaten viable mice, which express catalytically impaired forms of SHP-1, indicating that these proteins are SHP-1 substrates. However, BIT and PIR-B are hypophosphorylated in motheaten macrophages, which completely lack SHP-1 expression. These data suggest a model in which SHP-1 dephosphorylates specific sites on BIT and PIR-B while protecting other sites from dephosphorylation via its SH2 domains. Finally, BIT and PIR-B associate with two tyrosyl phosphoproteins and a tyrosine kinase activity. Tyrosyl phosphorylation of these proteins and the level of the associated kinase activity are increased in the absence of SHP-1. Our data suggest that BIT and PIR-B recruit multiple signaling molecules to receptor complexes, where they are regulated by SHP-1 and/or SHP-2.Protein tyrosine phosphatases (PTPs) and protein tyrosine kinases (PTKs) control the level of tyrosyl phosphorylation on cellular proteins (reviewed in references 38, 52, and 56). Although many substrates for PTKs have been identified, the specific targets of individual PTP family members, along with the consequences of protein dephosphorylation for cellular physiology, remain largely unknown. The finding that some PTPs possess SH2 domains suggested that these molecules might be recruited to specific phosphotyrosyl (pY) sites (via their SH2 domains), where their PTP domains could catalytically amplify or terminate phosphotyrosine-mediated signals (14, 37). Two vertebrate SH2-containing PTPs (SHPs), SHP-1 and SHP-2 (1), have been cloned and characterized (reviewed in reference 37). Despite their structural similarity, SHP-1 and SHP-2 appear to possess distinct biological functions (reviewed in references 3, 36 to 38, 52, and 56). SHP-2 is expressed ubiquitously and typically transmits positive (i.e., signal-enhancing) signals downstream of receptor tyrosine kinases, cytokine receptors, and multichain immune recognition receptors, although recent work suggests that it may have negative (i.e., signal-attenuating) effects in some pathways (33, 54). In contrast, SHP-1 is expressed predominantly in hematopoietic cells, where it negatively regulates multiple growth factor and cytokine signaling pathways (reviewed in references 36, 38 and 56).Our current understanding of the role played by S...

DIGE is a protein labelling and separation technique allowing quantitative proteomics of two or more samples by optical fluorescence detection of differentially labelled proteins that are electrophoretically separated on the same gel. DIGE is an alternative to quantitation by MS-based methodologies and can circumvent their analytical limitations in areas such as intact protein analysis, (linear) detection over a wide range of protein abundances and, theoretically, applications where extreme sensitivity is needed. Thus, in quantitative proteomics DIGE is usually complementary to MS-based quantitation and has some distinct advantages. This review describes the basics of DIGE and its unique properties and compares it to MS-based methods in quantitative protein expression analysis.

Purpose Biomarkers for the early detection of pancreatic cancer are urgently needed. The primary objective of this study was to evaluate whether increased levels of serum CA19-9, CA125, CEACAM1 and REG3A are present prior to clinical presentation of pancreatic cancer and to assess the performance of combined markers for early detection and prognosis. Experimental Design This nested case control study within UKCTOCS included 118 single- and 143 serial-serum samples from 154 post-menopausal women who were subsequently diagnosed with pancreatic cancer and 304 matched non-cancer controls. Samples were split randomly into independent training and test sets. CA19-9, CA125, CEACAM1 and REG3A were measured using ELISA and/or CLIA. Performance of markers to detect cancers at different times prior to diagnosis and for prognosis was evaluated. Results At 95% specificity, CA19-9 (>37 U/mL) had a sensitivity of 68% up to 1 year, and 53% up to 2 yrs before diagnosis. Combining CA19-9 and CA125 improved sensitivity as CA125 was elevated (>30 U/mL) in ~20% of CA19-9-negative cases. CEACAM1 and REG3A were late markers adding little in combined models. Average lead times of 20-23 months were estimated for test-positive cases. Pre-diagnostic levels of CA19-9 and CA125 were associated with poor overall survival (HR 2.69 and 3.15, respectively). Conclusions CA19-9 and CA125 have encouraging sensitivity for detecting pre-clinical pancreatic cancer and both markers can be used as prognostic tools. This work challenges the prevailing view that CA19-9 is up-regulated late in the course of pancreatic cancer development.