One of the major difficulties in mining low abundance biomarkers from serum or plasma is due to the fact that a small number of proteins such as albumin, alpha2-macroglobulin, transferrin, and immunoglobulins, may represent as much as 80% of the total serum protein. The large quantity of these proteins makes it difficult to identify low abundance proteins in serum using traditional 2-dimensional electrophoresis. We recently used a combination of multidimensional liquid chromatography and gel electrophoresis coupled to matrix-assisted laser desorption/ionization-quadrupole-time of flight and Ion Trap liquid chromatography-tandem mass spectrometry to identify protein markers in sera of Alzheimer's disease (AD), insulin resistance/type-2 diabetes (IR/D2), and congestive heart failure (CHF) patients. We identified 8 proteins that exhibit higher levels in control sera and 36 proteins that exhibit higher levels in disease sera. For example, haptoglobin and hemoglobin are elevated in sera of AD, IR/D2, and CHF patients. The levels of several other proteins including fibrinogen and its fragments, alpha 2-macroglobulin, transthyretin, pro-platelet basic protein, protease inhibitors clade A and C, as well as proteins involved in the classical complement pathway such as complement C3, C4, and C1 inhibitor, were found to differ between IR/D2 and control sera. The sera levels of proteins, such as the 10 kDa subunit of vitronectin, alpha 1-acid glycoprotein, apolipoprotein B100, fragment of factor H, and histidine-rich glycoprotein were observed to be different between AD and controls. The differences observed in these biomarker candidates were confirmed by Western blot and the enzyme-linked immunosorbent assay. The biological meaning of the proteomic changes in the disease states and the potential use of these changes as diagnostic tools or for therapeutic intervention will be discussed.

Mining biomarkers in human sera using proteomic tools

Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance suggests that their genes may have been subject to adaptive evolution. We have estimated the consequences of selection on rodent pheromones, their receptors, and olfactory receptors. These families were chosen on the basis of multiple gene duplications since the common ancestor of rat and mouse. For each family, codons were identified that are likely to have been subject to adaptive evolution. The majority of such sites are situated on the solvent-accessible surfaces of putative pheromones and the lumenal portions of their likely receptors. We predict that these contribute to physicochemical and functional diversity within pheromone-receptor interaction sites.

/pdf/evolution-and-comparative-genomics-of-odorant-and-pheromone-24yb7utuwe.pdf

Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents.

Lymphocyte Antigen 6 (Ly-6) superfamily members are cysteine-rich, generally GPI-anchored cell surface proteins, which have definite or putative immune related roles. There are 27 members of this family described so far in the human genome and 37 in the mouse. Five of them are clustered in the class III region of the human and mouse MHCs. Following computational analyses, we functionally characterized the encoded proteins by creating epitope-tagged fusion constructs to determine molecular weight, complex formation, subcellular localization, post-translational modifications and ligand binding. We found that all human and mouse proteins were glycosylated, and most could form part of larger complexes. Human and mouse Ly6G6c and Ly6G6d, and mouse Ly6g6e were found to be GPI-anchored cell surface proteins, highly expressed at the leading edges of cells, on filopodia, which are normally involved in cell adhesion and migration. However, analysis of Ly6G5c and Ly6G5b indicated that they are potentially secreted proteins. Our results indicate that there are two subclusters of related Ly-6 proteins in this region of the MHC, with Ly6G6c, Ly6G6d, and Ly6G6e forming one and Ly6G5c and Ly6G5b forming another. In addition, by FACS analysis we have found that the potential ligands for human LY6G6C, LY6G6D, and LY6G5C are expressed on K562 cells, an undifferentiated megakaryocyte cell line, indicating a potential role in hematopoietic cell differentiation. This characterization of the five MHC class III region Ly-6 family members is of great relevance, as they represent 18% of the human Ly-6 protein family and 50% of the secreted ones.

/pdf/characterization-of-the-five-novel-ly-6-superfamily-members-3mh053d9rh.pdf

Characterization of the five novel Ly‐6 superfamily members encoded in the MHC, and detection of cells expressing their potential ligands

SLURP-1 (secreted mammalian Ly-6/urokinase plasminogen activator receptor-related protein-1) is a novel auto/paracrine cholinergic peptide that can bind to α(7)-nicotinic acetylcholine receptor (nAChR), a high Ca(2+)-permeable ion channel coupled to regulation of nuclear factor-κB (NF-κB) expression. Elucidation of intracellular signaling events elicited by SLURP-1 is crucial for understanding the molecular mechanism of functioning of this novel hormone-like peptide that alters vital cell functions and can protect from tumorigenic transformation. In this study, we sought to dissect out the role of α(7)-nAChR in mediating the biologic effects of recombinant SLURP-1 on the immortalized line of human oral keratinocytes Het-1A. A multifold upregulation of the NF-κB expression at the mRNA and protein levels by SLURP-1 was only slightly diminished due to elimination of Na(+), whereas in Ca(2+)-free medium the effect of SLURP-1 was inhibited by >50%. Both in the absence of extracellular Ca(2+) and in the presence of Cd(2+) or Zn(2+), the SLURP-1-dependent elevation of NF-κB was almost completely blocked by inhibiting MEK1 activity. Downstream of α(7)-nAChR, the SLURP-1 signaling coupled to upregulation of NF-κB also involved Jak2 as well as Ca(2+)/calmodulin-dependent kinase II (CaMKII) and protein kinase C (PKC), whose inhibition significantly (P < 0.05) reduced the SLURP-1-induced upregulation of NF-κB. The obtained results indicated that activation of α(7)-nAChR by SLURP-1 leads to upregulation of the NF-κB gene expression due to activation of the Raf-1/MEK1/ERK1/2 cascade that proceeds via two complementary signaling pathways. One is mediated by the Ca(2+)-entry dependent CaMKII/PKC activation and another one by Ca(2+)-independent involvement of Jak2. Thus, there exists a previously not appreciated network of noncanonical auto/paracrine ligands of nAChR of the Ly-6 protein family, which merits further investigations.

Upregulation of nuclear factor-κB expression by SLURP-1 is mediated by α7-nicotinic acetylcholine receptor and involves both ionic events and activation of protein kinases

Urinary proteomics has become one of the most attractive subdisciplines in clinical proteomics as the urine is an ideal source for the discovery of noninvasive biomarkers for kidney and nonkidney diseases. This field has been growing rapidly as indicated by >80 original research articles on urinary proteome analyses appearing since 2001, of which 28 (approximately 1/3) had been published within the year 2006. The most common technologies used in recent urinary proteome studies remain gel-based methods (1-DE, 2-DE and 2-D DIGE), whereas LC-MS/MS, SELDI-TOF MS, and CE-MS are other commonly used techniques. In addition, mass spectrometric immunoassay (MSIA) and array technology have also been applied. This review provides an extensive but concise summary of recent applications of urinary proteomics. Proteomic analyses of dialysate and ultrafiltrate fluids derived from renal replacement therapy (or artificial kidney) are also discussed.

Recent progress in urinary proteomics.

A proteomic study of rat urine was undertaken using two-dimensional gel electrophoresis, microbore high performance liquid chromatography, mass spectrometry and N-terminal sequencing. Five known urinary proteins were identified but two novel peptide fragments matched a large number of rat expressed sequence tags (ESTs) from a liver library. By combining protein chemical and nucleotide data, two 101-residue open reading frames with 90% amino acid identity were determined, rat urinary protein 1 (RUP-1) and RUP-2. The data established signal peptide removal and provided evidence for N-glycosylation. A third related sequence, rat spleen protein (RSP-1) was confirmed from EST searches. These three proteins have been submitted to SWISS-PROT as P81827, P81828 and Q9QXN2, respectively. A fourth novel homologue was found in porcine and bovine ESTs from embryo libraries. Alignment with known homologues showed conserved cysteine positions characteristic of a secreted subfamily of Ly-6 proteins. In two cases, antineoplastic urinary protein and caltrin, these homologues have unverified functional annotations. The RUP sequences showed high scoring matches to three unrelated rat mRNAs subsequently established to be chimeric. Two of these share extended sectional identity to RUP-1 but the third may represent another novel Ly-6 homologue. These chimeras have caused serious annotation errors in secondary databases.

The characterisation of novel secreted Ly-6 proteins from rat urine by the combined use of two-dimensional gel electrophoresis, microbore high performance liquid chromatography and expressed sequence tag data.

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The characterisation of novel secreted Ly-6 proteins from rat urine by the combined use of two-dimensional gel electrophoresis, microbore high performance liquid chromatography and expressed sequence tag data.