A large-scale multi-center independent validation study of a panel of seven biomarkers for the detection of ovarian cancer

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Background: Previously we discovered seven serum biomarkers: ITIH4, transthyretin, ApoA1, CTAPIII, hepcidin, transferrin, and SAA, for the detection of ovarian cancer. They are fragments, cleavages, or PTMs of circulating proteins that are difficult to measure by conventional immunoassays. Using optimzed mass spectrometry assays, we evaluated these biomarkers in a large-scale multi-center study. Methods: A total of 607 serum samples from five sites were analyzed using SELDI TOF-MS protocols optimized for the seven biomarkers. They included 234 women with benign gynecologic diseases, and 373 patients with invasive epithelial ovarian cancer (101 early stage, 231 late stage, and 40 stage unknown). Among them, 165 benigns and 228 cancers had a CA125 available at time of analysis. The median and quartiles of CA125 for benign, early stage, and late or unknown stage were 26/11/57 IU, 80/22/434 IU, and 234/40/1114 IU, respectively. The biomarkers were assessed individually using the Mann-Whitney U Test. A linear composite index was derived in an unsupervised fashion using data from one site and then calculated for the remaining data using the fixed formula. ROC curve analyses were performed on data from individual sites and all sites combined. Results: All seven biomarkers individually demonstrated statistically significant differentiating power, and the majority had p-value<0.00001. AUCs of the composite index in ROC analyses for the six sites were 0.602, 0.566, 0.821, 0.813, and 0.592 in detecting cancer at all stages from benign. On the combined data, the differences in AUC between the index and CA125 were not statistically significant for the detection of cancer at all stages (AUC=0.706 vs. 0.725) or early stages only (AUC=0.534 vs. 0.653). However, the index did better at the high-sensitivity range. At a fixed sensitivity of 86%, the specificity of the index was 34% (77/226) compared to CA125 at 26% (42/163). For early stage cases, at a fixed sensitivity of 84%, the specificity of the index was 24% (55/226) compared to CA125 at 14%% (22/163). Conclusions: We validated seven previously discovered biomarkers, individually and in combination. Prospective studies and assay development are under way to further characterize their clinical utility.

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Postoperative serum proteomic profiles may predict metastatic relapse in high-risk primary breast cancer patients receiving adjuvant chemotherapy

A total of 30-50% of early breast cancer (EBC) patients considered as high risk using standard prognostic factors develop metastatic recurrence despite standard adjuvant systemic treatment. A means to better predict clinical outcome is needed to optimize and individualize therapeutic decisions. To identify a protein signature correlating with metastatic relapse, we performed surface-enhanced laser desorption/ionization-time of flight mass spectrometry profiling of early postoperative serum from 81 high-risk EBC patients. Denatured and fractionated serum samples were incubated with IMAC30 and CM10 ProteinChip arrays. Several protein peaks were differentially expressed according to clinical outcome. By combining partial least squares and logistic regression methods, we built a multiprotein model that correctly predicted outcome in 83% of patients. The 5-year metastasis-free survival in 'good prognosis' and 'poor prognosis' patients as defined using the multiprotein index were strikingly different (83 and 22%, respectively; P<0.0001, log-rank test). In a multivariate Cox regression including conventional pathological factors and multiprotein index, the latter retained the strongest independent prognostic significance for metastatic relapse. Major components of the multiprotein index included haptoglobin, C3a complement fraction, transferrin, apolipoprotein C1 and apolipoprotein A1. Therefore, postoperative serum protein pattern may have an important prognostic value in high-risk EBC.

Protein biochips for differential profiling

Progress has been made in utilizing ProteinChip technology to profile and compare protein expression in normal and diseased states, particularly in the areas of cancer, infectious disease and toxicology. The past year has also seen the development of several novel chip types designed to analyze proteins in a fashion analogous to the array-based format of DNA microarrays. Some of these platforms may be used for differential profiling.

Proteomic strategies for biomarker identification: progress and challenges

The simplest definition of a biomarker is a molecule that indicates an alteration in physiology from normal. A more practical definition of a biomarker would require clinical utility of this molecule. In this sense, the biomarker would specifically and sensitively reflect a disease state and could be used for diagnosis as well as for disease monitoring during and following therapy. The need for such biomarkers in all clinical fields is urgent, since the current arsenal of biomarkers is sadly deficient and, in most cases, non-specific. In this review, we discuss strategies that use a proteomics approach to identify novel biomarkers and give examples of recent studies employing these strategies.

Identification of a novel alternatively spliced septin

Septins are a family of cytoskeletal proteins involved in cytokinesis, targeting of proteins to specific sites on the plasma membrane, and cellular morphogenesis. While many aspects of their function in cytokinesis in yeast cells have been investigated, the function of septins in mammalian cells is less well understood. For example, septins are present in post-mitotic neurons, suggesting they have other roles in, for example, establishing cell polarity. The full extent of the septin gene family is not known in mammalian cells. To better understand the septin gene family, we have cloned and characterized a novel mammalian septin.

Identification of a Torpedo homolog of Sam68 that interacts with the synapse organizing protein rapsyn

Nicotinic acetylcholine receptors (nAChRs) are initially expressed diffusely on the surface of myotubes and, in response to neuronally derived factors, cluster at the endplate to a final concentration of approximately 10000/microm2. The synaptic peripheral membrane protein rapsyn has been shown to mediate clustering of nAChRs in several systems. Here we describe the use of the yeast two-hybrid system to identify proteins that can interact with rapsyn. One of the clones we have identified is a Torpedo californica homolog of the Src-associated in mitosis protein (Sam68). We further show that Sam68, like rapsyn, is localized at the neuromuscular junction.

Identification of a dynein molecular motor component in Torpedo electroplax; binding and phosphorylation of Tctex-1 by Fyn

The microtubule protein Tctex-1 was cloned from Torpedo electroplax, a biochemical model of the neuromuscular junction, using the unique domain of Fyn in the yeast two hybrid system. Binding of Tctex-1 and Fyn also occurred in vitro. Torpedo Tctex-1 was contained within the molecular motor protein dynein. A Src class kinase was also complexed with dynein. Tctex-1 was enriched in electric organ vs. skeletal muscle, was present in the postsynaptic membrane, and coprecipitated with the acetylcholine receptor. The sequence of Tctex-1 contained a tyrosine phosphorylation motif and Tctex-1 could be phosphorylated by Fyn in vitro and in vivo. These data demonstrated that Tctex-1-containing dynein is a cytoskeletal element at the acetylcholine receptor-enriched postsynaptic membrane and suggested that Tctex-1 may be a substrate for Fyn.

Characterization of the tyrosine phosphorylation and distribution of dystrobrevin isoforms

Dystrobrevin, a member of the dystrophin family of proteins, was initially identified as a major tyrosine phosphorylated synaptic protein in the electric organ of Torpedo californica. In this paper, we show that the major sites of tyrosine phosphorylation of Torpedo dystrobrevin are within its C-terminus, on Tyr-693 and Tyr-710. Cloning of the mammalian homologue of dystrobrevin has recently shown that this phosphotyrosine containing tail, or PYCT, is subject to alternative splicing. To compare the expression and distribution of PYCT- and PYCT+ splice variants, we generated antibodies against different regions of dystrobrevin. Here we show that the PYCT- isoform of 62 kDa is expressed at high levels in all tissues examined. In contrast, PYCT+ isoforms are expressed primarily in brain and muscle, where they are concentrated at synapses. Moreover, PYCT+ isoforms associate more tightly with the membrane and with syntrophin, another synaptically enriched protein. These results suggest that PYCT+ isoforms of dystrobrevin are specialized components of the dystroglycan complex which render the complex sensitive to regulation by tyrosine kinases.

Splice variant-specific interaction of the NMDA receptor subunit NR1 with neuronal intermediate filaments

NMDA receptors are excitatory neurotransmitter receptors critical for synaptic plasticity and neuronal development in the mammalian brain. These receptors are found highly concentrated in the postsynaptic membrane of glutamatergic synapses. To investigate the molecular mechanisms underlying NMDA receptor localization, we used the yeast two-hybrid system to identify proteins expressed in the brain that interact with the NMDA receptor subunit NR1. Here we report that the 68 kDa neurofilament subunit NF-L directly interacts with the NR1 subunit. This interaction occurs between the cytoplasmic C-terminal domain of NR1 and the rod domain of NF-L. However, NR1 splice variants lacking the first C-terminal exon cassette (C1) failed to associate with NF-L. Immunogold electron microscopy revealed a preferential localization of NR1 at the ends of in vitro-assembled neurofilaments. Overexpression of C1 cassette-containing NR1 constructs in fibroblast cells disrupted the assembly of recombinant neurofilaments. In addition, NR1 and NF-L cofractionated in detergent-treated rat brain synaptic plasma membranes. Furthermore, NR1 and NF-L colocalize in the dendrites and growth cones of cultured hippocampal neurons. These results demonstrate the splice variant-specific association of NR1 with neurofilaments and suggest a possible mechanism for anchoring or localizing NMDA receptors in the neuronal plasma membrane.

FKBP12 binds the inositol 1,4,5-trisphosphate receptor at leucine-proline (1400-1401) and anchors calcineurin to this FK506-like domain

The immunophilin FKBP12 is one of the most abundant and conserved proteins in biology. It is the primary receptor for the immunosuppressant actions of the drug FK506 in whose presence FKBP12 binds to and inhibits calcineurin, disrupting interleukin formation in lymphocytes. The physiologic functions of FKBP12 are less clear, although the protein has been demonstrated to physiologically interact with the inositol 1,4,5-trisphosphate receptor (IP3R), the ryanodine receptor, and the type 1 transforming growth factor beta receptor. We now report that FKBP12 binds the IP3R at residues 1400-1401, a leucyl-prolyl dipeptide epitope that structurally resembles FK506. We further demonstrate that binding to IP3R at this site enables FKBP12 to interact with calcineurin, presumably to anchor the phosphatase to IP3R and modulate the receptor's phosphorylation status. We propose that FK506 promotes an FKBP12-calcineurin interaction by mimicking structurally similar dipeptide epitopes present within proteins that use FKBP12 to anchor calcineurin to the appropriate physiologic substrates.

GRIP: a synaptic PDZ domain-containing protein that interacts with AMPA receptors

AMPA glutamate receptors mediate the majority of rapid excitatory synaptic transmission in the central nervous system and play a role in the synaptic plasticity underlying learning and memory. AMPA receptors are heteromeric complexes of four homologous subunits (GluR1-4) that differentially combine to form a variety of AMPA receptor subtypes. These subunits are thought to have a large extracellular amino-terminal domain, three transmembrane domains and an intracellular carboxy-terminal domain. AMPA receptors are localized at excitatory synapses and are not found on adjacent inhibitory synapses enriched in GABA(A) receptors. The targeting of neurotransmitter receptors, such as AMPA receptors, and ion channels to synapses is essential for efficient transmission. A protein motif called a PDZ domain is important in the targeting of a variety of membrane proteins to cell-cell junctions including synapses. Here we identify a synaptic PDZ domain-containing protein GRIP (glutamate receptor interacting protein) that specifically interacts with the C termini of AMPA receptors. GRIP is a new member of the PDZ domain-containing protein family which has seven PDZ domains and no catalytic domain. GRIP appears to serve as an adapter protein that links AMPA receptors to other proteins and may be critical for the clustering of AMPA receptors at excitatory synapses in the brain.

Rapsyn clusters and activates the synapse-specific receptor tyrosine kinase MuSK

Nerve-induced clustering of the nicotinic acetylcholine receptor (AChR) requires rapsyn, a synaptic peripheral membrane protein, as well as protein-tyrosine kinase activity. Here, we show that rapsyn induces the clustering of the synapse-specific receptor-tyrosine kinase MuSK in transfected QT-6 fibroblasts. Furthermore, rapsyn stimulates the autophosphorylation of MuSK, leading to a subsequent MuSK-dependent increase in cellular tyrosine phosphorylation. Moreover, rapsyn-activated MuSK specifically phosphorylated the AChR beta subunit, the same subunit that is tyrosine phosphorylated during innervation or agrin treatment of muscle. These results suggest rapsyn may mediate the synaptic localization of MuSK in muscle and that MuSK may play an important role in the agrin-induced clustering of the AChR.

Laser desorption/Fourier transform mass spectrometry of steroids

Mass spectra of six representative underivatized steroids and three parent hydrocarbons were obtained using laser desorption/Fourier transform (LD/FT) mass spectrometry. The carbonyl steroids, with the exception of aldosterone, yielded abundant [M + H]+ ions. For cholesterol, a major fragment ion was that corresponding to dehydration. The hydrocarbons produced [M + H]+, M+ and [M - H]+ ions, in addition to expected alkyl cleavage ions including those resulting from methyl loss. The LD/FT mass spectra of all were qualitatively similar to electron ionization spectra, but showed somewhat less fragmentation.