An integrated approach to prognosis using protein microarrays and nonparametric methods

Over the past several years, multivariate approaches have been developed that address the problem of disease diagnosis. Here, we report an integrated approach to the problem of prognosis that uses protein microarrays to measure a focused set of molecular markers and non-parametric methods to reveal non-linear relationships among these markers, clinical variables, and patient outcome. As proof-of-concept, we applied our approach to the prediction of early mortality in patients initiating kidney dialysis. We found that molecular markers are not uniformly prognostic, but instead vary in their value depending on a combination of clinical variables. This may explain why reports in this area aiming to identify prognostic markers, without taking into account clinical variables, are either conflicting or show that markers have marginal prognostic value. Just as treatments are now being tailored to specific subsets of patients, our results show that prognosis can also benefit from a 'personalized' approach.

IKAP/hELP1 deficiency in the cerebrum of familial dysautonomia patients results in down regulation of genes involved in oligodendrocyte differentiation and in myelination

The gene affected in the congenital neuropathy familial dysautonomia (FD) is IKBKAP that codes for the IKAP/hELP1 protein. Several different functions have been suggested for this protein, but none of them have been verified in vivo or shown to have some link with the FD phenotype. In an attempt to elucidate the involvement of IKAP/hELP1 in brain function, we searched for IKAP/hELP1 target genes associated with neuronal function. In a microarray expression analysis using RNA extracted from the cerebrum of two FD patients as well as sex and age matched controls, no genes were found to be upregulated in the FD cerebrum. However, 25 genes were downregulated more than 2-fold in the cerebrum of both the male FD child and female FD mature woman. Thirteen of them are known to be involved in oligodendrocyte development and myelin formation. The down regulation of all these genes was verified by real-time PCR. Four of these genes were also confirmed to be downregulated at the protein level. These results are statistically significant and have high biological relevance, since seven of the downregulated genes in the cerebrum of the FD patients were shown by others to be upregulated during oligodendrocyte differentiation in vitro. Our results therefore suggest that IKAP/hELP1 may play a role in oligodendrocyte differentiation and/or myelin formation.

Molecular mechanisms of thrombin-induced interleukin-8 (IL-8/CXCL8) expression in THP-1-derived and primary human macrophages

Under normal conditions, macrophages provide essential innate immune surveillance in tissues. These cells also play key functions during wound healing and in pathological conditions. When macrophages are exposed to thrombin, an enzyme released from leaky blood vessels, they are stimulated to produce inflammatory cytokines, which are critical for wound healing and can also facilitate tumor growth and invasion. Using antibody cytokine arrays, we identified IL-8/CXCL8, a chemokine that plays important functions in inflammation and angiogenesis and consequently in healing and tumor development, as one of the cytokines that is highly stimulated in macrophages by thrombin. Here, we investigated the signal transduction mechanism by which thrombin stimulates IL-8/CXCL8 expression in THP-1-derived and primary human macrophages. We show that JNK is a crucial mediator of the thrombin signaling pathways in macrophages, and the activation of JNK is dependent on stimulation of the Rho small GTPase. The thrombin-induced Rho/JNK cascade is a novel signaling cascade for IL-8/CXCL8 transcription activation. Understanding the molecular mechanism by which thrombin controls the expression of inflammatory cytokines in macrophages can lead to therapeutic interventions, which can provide better management of healing, inflammation, and tumorigenesis.

Topo-Proteomic in situ Analysis of Psoriatic Plaque under Efalizumab Treatment

In a pilot study 6 psoriasis patients were treated over 12 weeks with efalizumab targeting the CD11a subunit of LFA-1. The treatment was well tolerated. Five of these patients proved to be responders with an average decrease in psoriasis area and severity index (PASI) from 21.3 +/- 5.4 (day 0) to 3.9 +/- 0.6 (week 12). The nonresponder was subsequently successfully treated with cyclosporin. Skin biopsies were taken before and after efalizumab treatment and subjected to Multi-Epitope Ligand Cartography (MELC) robot microscopy. A MELC library of 46 antibodies including FITC-labeled efalizumab was chosen focusing upon inflammatory epitopes. Quantification of marker expression was performed using a special adaptation to the needs of skin tissue in terms of pixel events normalized to a standardized horizontal skin width of 100 mum. The before-versus-after comparison for the responders revealed at the 'single epitope level' of MELC analysis a significant decrease (p < 0.05) in epidermal thickness (represented by pan-cytokeratin, CD71, CD138), of the expression of common leukocyte antigen (CD45), T-cell markers (CD2, CD4, CD8, CD45R0), CD11a, efalizumab binding site (EfaBS), and CD58. At the 'EfaBS-centered, double colocation level' a corresponding decrease was observed for CD2, CD3, CD4, CD8, CD11a, CD13, CD26, CD44, CD45, CD45R0, CD54, CD62L, HLA-DR, and TIA-1. MELC analysis at the 'multicombinatorial level' revealed predominant combinatorial molecular phenotype (CMP) motifs, which showed an efalizumab treatment-dependent significant decrease. These CMP motifs were defined as toponomic combinations of lead markers for (i) leukocytes in general (CD45), (ii) T cells (CD2, CD3, CD4, CD45R0, CD45RA), (iii) macrophages (CD68), (iv) cell activation (CD13, CD26, HLA-DR), and (v) cell adhesion (CD11a, EfaBS). Thirty-five of the most relevant 50 CMP motifs were directly related to the T-cell type. A descriptive statistical analysis of the nonresponder before treatment showed a below-responder range degree of expression for CD4, CD8, CD44 (H-CAM), CD56, CD62L, HLA-DQ, and also for these epitopes in colocation with EfaBS. In the nonresponder and before treatment we observed an above-responder range degree of expression for CD54 (ICAM-1) as LFA-1 ligand. In conclusion, the topo-proteomic data provide new diversified insights into the pleiotropic cellular dynamics in psoriatic skin lesions under effective efalizumab treatment. Moreover, the data may be relevant to the future development of possible strategies for individual prediction of efalizumab treatment response or nonresponse.

Identification of an orthogonal peptide binding motif for biarsenical multiuse affinity probes

Biarsenical multiuse affinity probes (MAPs) complexed with ethanedithiol (EDT) permit the selective cellular labeling of proteins engineered with tetracysteine motifs, but are limited by the availability of a single binding motif (i.e., CCPGCC or PG tag) that prevents the differential labeling of coexpressed proteins. To overcome this problem, we have used a high-throughput peptide screen to identify an alternate binding motif (i.e., CCKACC or KA tag), which has a similar brightness to the classical sequence upon MAP binding, but displays altered rates and affinities of association that permit the differential labeling of these peptide sequences by the red probe 4,5-bis(1,3,2-dithiarsolan-2-yl)-resorufin (ReAsH-EDT2) or its green cognate 4',5'-bis(1,3,2-dithoarsolan-2-yl)fluorescein (FLAsH-EDT2). The utility of this labeling strategy was demonstrated following the expression of PG- and KA-tagged subunits of RNA polymerase in E. coli. Specific labeling of two subunits of RNA polymerase in cellular lysates was achieved, whereby ReAsH-EDT2 is shown to selectively label the PG-tag on RNA polymerase alpha-subunit prior to the labeling of the KA-tag sequence of the beta-subunit of RNA polymerase with FlAsH-EDT2. These results demonstrate the ability to selectively label multiple individual proteins with orthogonal sequence tags in complex cellular lystates with spectroscopically distinct MAPs, and indicate the absolute specificity of ReAsH to target expressed proteins with essentially no nonspecific binding interactions.

Claudin-1 immunohistochemistry for distinguishing malignant from benign epithelial lesions of prostate

BACKGROUND

Claudins are a family of approximately 23 integral membrane tight junction (TJ) proteins that maintain cell polarity and paracellular barrier functions in epithelial and endothelial cells. Although Claudin-1 was demonstrated to be typically downregulated in various cancers, the precise expression patterns of this protein in normal and neoplastic tissues remain poorly characterized.

METHODS

Using immunohistochemistry, the expression of Claudin-1 was investigated in prostate tissue samples arranged in a tissue microarray (TMA) format and comprising elements of normal prostatic epithelium (n = 6), benign prostatic hyperplasia (BPH; n = 38), prostatic intraepithelial neoplasia (PIN; n = 11), and prostate adenocarcinoma (n = 48). The Claudin-1 expression pattern was compared with that of the basal cell-specific markers, p63, and HMW cytokeratin (34betaE12), by employing double-labeling techniques in conjunction with image analysis methods utilizing color deconvolution algorithms.

RESULTS

In benign prostatic epithelium, pronounced Claudin-1 expression was observed in the basal cell layer with no staining in luminal cells. Prostate adenocarcinoma specimens from 98% (47/48) patients lacked Claudin-1 immunostaining, and no cases contained >5% immunopositive tumor cells.

CONCLUSIONS

Claudin-1 immunohistochemistry should be considered for use as a new diagnostic tool for distinguishing malignant from benign lesions of the prostate.

Autoantibody microarrays for biomarker discovery

Identification of autoantigens and the detection of autoantibody reactivity are useful in biomarker discovery and for explaining the role of important biochemical pathways in disease. Despite all of their potential advantages, the main challenge to working with autoantibodies is their sensitivity. Nevertheless, proteomics may hold the key to overcoming this limitation by providing the means to multiplex. Clearly, the ability to detect multiple autoantigens using a platform such as a high-density antigen microarray would improve sensitivity and specificity of detection for autoantibody profiling. The aims of this review are to: briefly describe the current status of antigen-autoantibody microarrays; provide examples of their use in biomarker discoveries; address current limitations; and provide examples and strategies to facilitate their implementation in the clinical setting.

Cytoskeletal protein transformation in HIV-1-infected macrophage giant cells

The mechanisms linking HIV-1 replication, macrophage biology, and multinucleated giant cell formation are incompletely understood. With the advent of functional proteomics, the characterization, regulation, and transformation of HIV-1-infected macrophage-secreted proteins can be ascertained. To these ends, we performed proteomic analyses of culture fluids derived from HIV-1 infected monocyte-derived macrophages. Robust reorganization, phosphorylation, and exosomal secretion of the cytoskeletal proteins profilin 1 and actin were observed in conjunction with productive viral replication and giant cell formation. Actin and profilin 1 recruitment to the macrophage plasma membrane paralleled virus-induced cytopathicity, podosome formation, and cellular fusion. Poly-l-proline, an inhibitor of profilin 1-mediated actin polymerization, inhibited cytoskeletal transformations and suppressed, in part, progeny virion production. These data support the idea that actin and profilin 1 rearrangement along with exosomal secretion affect viral replication and cytopathicity. Such events favor the virus over the host cell and provide insights into macrophage defense mechanisms used to contain viral growth and how they may be affected during progressive HIV-1 infection.

Elucidating the secretion proteome of human embryonic stem cell-derived mesenchymal stem cells

Transplantation of mesenchymal stem cells (MSCs) has been used to treat a wide range of diseases, and the mechanism of action is postulated to be mediated by either differentiation into functional reparative cells that replace injured tissues or secretion of paracrine factors that promote tissue repair. To complement earlier studies that identified some of the paracrine factors, we profiled the paracrine proteome to better assess the relevance of MSC paracrine factors to the wide spectrum of MSC-mediated therapeutic effects. To evaluate the therapeutic potential of the MSC paracrine proteome, a chemically defined serum-free culture medium was conditioned by MSCs derived from human embryonic stem cells using a clinically compliant protocol. The conditioned medium was analyzed by multidimensional protein identification technology and cytokine antibody array analysis and revealed the presence of 201 unique gene products. 86-88% of these gene products had detectable transcript levels by microarray or quantitative RT-PCR assays. Computational analysis predicted that these gene products will significantly drive three major groups of biological processes: metabolism, defense response, and tissue differentiation including vascularization, hematopoiesis, and skeletal development. It also predicted that the 201 gene products activate important signaling pathways in cardiovascular biology, bone development, and hematopoiesis such as Jak-STAT, MAPK, Toll-like receptor, transforming growth factor-beta, and mTOR (mammalian target of rapamycin) signaling pathways. This study identified a large number of MSC secretory products that have the potential to act as paracrine modulators of tissue repair and replacement in diseases of the cardiovascular, hematopoietic, and skeletal tissues. Moreover our results suggest that human embryonic stem cell-derived MSC-conditioned medium has the potency to treat a variety of diseases in humans without cell transplantation.

All-trans retinoic acid induces different immunophenotypic changes on human HL60 and NB4 myeloid leukaemias

All-trans retinoic acid (ATRA) is used to treat patients with acute promyelocytic leukaemia (APL), inducing APL cells to differentiate into abnormal neutrophils. To investigate the possible relationship between the chromosome translocation t(15;17) found in APL and ATRA treatment, the human myeloid leukaemia cell lines HL60 and NB4, that are PML-RARalpha negative and positive, respectively, were treated with ATRA and immunophenotyped using a CD antibody microarray. For HL60 cells, ATRA induced major increases in descending order of CD38, CD11b, CD45RO, CD11c, CD54 and CD36 with repression of CD117 and CD44. For NB4 cells, ATRA induced major increases in descending order of CD11c, CD54, CD11a, CD11b, CD53, CD65, CD138, CD66c and T-cell receptor alpha/beta (TCRalpha/beta), with repression of CD38 and CD9. The induction of a number of these CD antigens is consistent with the known differentiation of these leukaemias to abnormal neutrophils. Approximately half of the antigens up-regulated by ATRA on NB4 cells were adhesion molecules, including CD11a, CD11b, CD11c, CD54, CD66c and CD138, consistent with the increased adhesiveness of leukaemia cells observed for APL patients treated with ATRA. On HL60 cells, ATRA induced expression of CD38, CD43 and CD45RO and repressed CD117, while the converse was true on NB4 cells that contain chimeric PML-RARalpha. For NB4 cells, ATRA induced some remarkable increases in CD antigens not seen for HL60: CD14 (16.6-fold), CD32 (27.8), CD53 (20.5), CD65 (139), CD66c (79.7), CD126 (15.1), and CD138 (57.6). The expression of these antigens may be regulated by PML-RARalpha in the presence of ATRA. Such CD antigens could be targets for synergistic treatment of APL with therapeutic antibodies following ATRA treatment.

Comparative proteomic expression profile in all-trans retinoic acid differentiated neuroblastoma cell line

Neuroblastoma (NB) is an infant tumor which frequently differentiates into neurons. We used two-dimensional differential in-gel electrophoresis (2D-DIGE) to analyze the cytosolic and nuclear protein expression patterns of LAN-5 cells following neuronal differentiating agent all-trans-retinoic acid treatment. We identified several candidate proteins, from which G beta2 and Prefoldin 3 may have a role on NB development. These results strength the use of proteomics to discover new putative protein targets in cancer.

Proteomic expression profiling of breast cancer

Breast cancer is one of the most common cancers observed in women in industrialized Western countries. The development of novel diagnostic methods and the application of modern systemic therapies have significantly optimized early detection and therapy of breast cancer. However, many patients are currently overtreated. Traditionally, tumours have been categorized on the basis of histopathological criteria. However, staining pattern and intensity of cancer cells are not sufficient to reflect the molecular events driving tumour development and progression. Therefore, new genomic, transcriptomic and proteomic techniques are applied to clinical samples aiming to identify new targets for a therapy tailored for an individual patient. After an introduction to common genomic and transcriptomic profiling technologies and their relevance for clinical use, we will focus on analytical and preanalytical applications for the identification of new therapeutic targets by protein profiling, with a special emphasis on two-dimensional gel-technologies (2D-PAGE), particularly as they apply to the study of breast cancer.

[Identification of biomarkers and therapeutic targets for renal cell cancer using ProteinChip technology]

In order to understand tumour biology in its complexity, it is necessary to investigate the proteomics in addition to the DNA and RNA level. SELDI-TOF-MS represents a new technology allowing a highly sensitive high-throughput analysis to detect specific protein profiles. In renal cancer, it was possible to define specific protein patterns in serum. Several proteins have been identified, i.e. serum amyloid alpha (SAA). Analysis of tumour tissues leads to a better understanding of tumour biology and provides the basis for differential classification and evaluation of prognosis. Investigation of the proteome concerning therapy results opens up the possibility of assessing downstream effects on the one hand and identifying biomarkers for selection of patients and therapy monitoring on the other hand. This review presents the first results for renal cancer.

Atomic resolution insight into host cell recognition by Toxoplasma gondii

The obligate intracellular parasite Toxoplasma gondii, a member of the phylum Apicomplexa that includes Plasmodium spp., is one of the most widespread parasites and the causative agent of toxoplasmosis. Micronemal proteins (MICs) are released onto the parasite surface just before invasion of host cells and play important roles in host cell recognition, attachment and penetration. Here, we report the atomic structure for a key MIC, TgMIC1, and reveal a novel cell-binding motif called the microneme adhesive repeat (MAR). Using glycoarray analyses, we identified a novel interaction with sialylated oligosaccharides that resolves several prevailing misconceptions concerning TgMIC1. Structural studies of various complexes between TgMIC1 and sialylated oligosaccharides provide high-resolution insights into the recognition of sialylated oligosaccharides by a parasite surface protein. We observe that MAR domains exist in tandem repeats, which provide a highly specialized structure for glycan discrimination. Our work uncovers new features of parasite-receptor interactions at the early stages of host cell invasion, which will assist the design of new therapeutic strategies.

Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast

Ubiquitin-protein ligases (E3s) are responsible for target recognition and regulate stability, localization or function of their substrates. However, the substrates of most E3 enzymes remain unknown. Here, we describe the development of a novel proteomic in vitro ubiquitination screen using a protein microarray platform that can be utilized for the discovery of substrates for E3 ligases on a global scale. Using the yeast E3 Rsp5 as a test system to identify its substrates on a yeast protein microarray that covers most of the yeast (Saccharomyces cerevisiae) proteome, we identified numerous known and novel ubiquitinated substrates of this E3 ligase. Our enzymatic approach was complemented by a parallel protein microarray protein interaction study. Examination of the substrates identified in the analysis combined with phage display screening allowed exploration of binding mechanisms and substrate specificity of Rsp5. The development of a platform for global discovery of E3 substrates is invaluable for understanding the cellular pathways in which they participate, and could be utilized for the identification of drug targets.

Construction of hybrid bilayer membrane (HBM) Biochips and characterization of the cooperative binding between cytochrome-c and HBM

We constructed multi-channel hybrid bilayer membrane (HBM) biochips and characterized them by surface plasmon resonance imaging. Each channel in the biochip was prepared using vesicles with different proportions of negative, neutral, and positive lipids. The HBM surfaces were tested by interaction with two globular proteins that recognize surfaces covered with opposite charges. Spots modified with the same HBM show responses within a relative standard deviation of 10% or smaller. These devices were also used to study in detail the interaction between cytochrome-c (cyt-c) and HBMs. Cooperative binding between cyt-c and negative HBMs was demonstrated. Using an adaptation of the Hill model, we calculated a Hill coefficient of 5 and a 10-fold increase in the binding constant with the increase in cyt-c concentration. We propose that this treatment can be used to evaluate the cooperative binding of surface proteins to membranes.

Ultrasensitive assays for proteins

Proteins are essential components of organisms and are involved in a wide range of biological functions. There are increasing demands for ultra-sensitive protein detection, because many important protein biomarkers are present at ultra-low levels, especially during the early stages of disease. Measuring proteins at low levels is also crucial for investigations of the protein synthesis and functions in biological systems. In this review, we summarize the recent developments of novel technology enabling ultrasensitive protein detection. We focus on two groups of techniques that involve either polymerase amplification of affinity DNA probes or signal amplification by the use of nano-/micro-materials. The polymerase-based amplification of affinity DNA probes indirectly improves the sensitivity of protein detection by increasing the number of detection molecules. The use of nano-/micro-materials conjugated to affinity probes enhances the measurement signals by using the unique electrical, optical, and catalytic properties of these novel materials. This review describes the basic principles, performances, applications, merits, and limitations of these techniques.

[Establishment of a diagnostic model of serum protein fingerprint pattern for esophageal cancer screening in high incidence area and its clinical value]

OBJECTIVE

To analyze the alterations of serum proteomic pattern in esophageal squamous cell carcinoma (ESCC) by SELDI-TOF-MS, to establish a diagnostic model of ESCC screening in high incidence area and investigate its clinical value.

METHODS

SELDI-TOF-MS and CM10 proteinChip were used to detect the serum proteomic patterns of 36 cases of ESCC and 38 healthy control subjects in high incidence area. The data were analyzed and a diagnostic model was established by using support vector machine (SVM). The diagnostic model was evaluated by leave-one-out cross validation.

RESULTS

At the molecular weight range of 2000 to 20,000, 31 protein peaks were significantly different between ESCC and controls (P < 0.01). A diagnostic model consisting of 4 protein peaks could do the best in diagnosis of ESCC and controls. The accuracy was 85.1%, sensitivity was 86.1%, specificity was 84.2%, and positive value was 83.8%.

CONCLUSION

The diagnostic model formed by 4 protein peaks, established in this study, can well distinguish ESCC from healthy subjects. It provides a new approach for ESCC screening in high incidence area.

The management of the patient with unexpected autoantibody positivity

Different autoantibodies are often measured simultaneously; this typically occurs when using indirect immunofluorescence on tissue sections or multiplex detection systems and may generate clinically "unexpected" positivities (i.e., without any relation to the disease under investigation). Their number is expected to increase with the development of microarray systems in autoantibody assays. In general, when examining patients with such unexpected findings, it is necessary to take into account that: a) autoantibody positivities are much more frequent than autoimmune diseases; b) the positive predictive value of an autoantibody positivity depends upon the diagnostic accuracy of the test and disease prevalence; c) autoantibodies may be risk factors for autoimmune disease or may also have a pathogenetic role by themselves. In this article we will highlight the possible problems raised by some relatively common situations, related to anti-nuclear, anti-thyroid, anti-phospholipid and anti-tissue transglutaminase autoantibodies. The need for specific strategies is outlined.

Mapping Putative Contact Sites Between Subunits in a Bacterial ATP-binding Cassette (ABC) Transporter by Synthetic Peptide Libraries

The maltose ATP-binding cassette transporter of Salmonella typhimurium is composed of the soluble periplasmic receptor, MalE, and a membrane-associated complex comprising one copy each of the pore-forming hydrophobic subunits, MalF and MalG, and of a homodimer of the ATP-hydrolyzing subunit, MalK. During the transport process the subunits are thought to undergo conformational changes that might transiently alter molecular contacts between MalFG and MalK(2). In order to map sites of subunit-subunit interactions we have used a comprehensive peptide mapping approach comprising large-scale microsynthesis of labelled probes and array techniques. In particular, we screened the binding of (i) MalFG-derived soluble biotinylated peptides to immobilized MalK, and (ii) radiolabelled MalK to MalFG-derived cellulose membrane-bound peptides. The first approach identified seven peptides (10mers) each of MalF and MalG that specifically bound to MalK. The peptides were localized to TMDs 3 and 6, periplasmic loop P4 and cytoplasmic loops C2 and C3 of MalF, while MalG-derived peptides localized to the N terminus, TMDs 4-6, periplasmic loop P1 and cytoplasmic loop C2. Peptides from C3 and C2, respectively, of MalF and MalG partially encompass the conserved EAA-motif, known to be crucial for interaction with MalK. These results were basically confirmed by screening MalFG-derived peptide arrays consisting of 16mers or 31mers with radiolabelled MalK. This approach also allowed us to perform complete substitutional analyses of peptides in question. The results led to the construction of MalFG variants that were subsequently analyzed for functional consequences in vivo. Growth experiments revealed that most of the mutations had no phenotype, suggesting that the mutated residues themselves are not critical but part of a discontinuous binding site. However, two novel mutations affecting residues from the EAA motifs of MalF (Ile417Glu) and MalG (Phe203Gln/Asn), respectively, displayed severe growth defects, indicating their functional importance. Together, these experimental outcomes identify specific molecular contacts made between MalK and MalFG that extend beyond the well-characterized EAA motif.

A multivariate analysis approach to the integration of proteomic and gene expression data

In order to understand even the simplest cellular processes, we need to integrate proteomic, gene expression and other biomolecular data. To date, most computational approaches aimed at integrating proteomics and gene expression data use direct gene/protein correlation measures. However, due to post-transcriptional and translational regulations, the correspondence between the expression of a gene and its protein is complicated. We apply a multivariate statistical method, co-inertia analysis (CIA), to visualise gene and proteomic expression data stemming from the same biological samples. Principal components analysis or correspondence analysis can be used for data exploration on single datasets. CIA is then used to explore the relationships between two or more datasets. We further explore the data by projecting gene ontology (GO) information onto these plots to describe the cellular processes in action. We apply these techniques to gene expression and protein abundance data from studies of the human malarial parasite life cycle and the NCI-60 cancer cell lines. In each case, we visualise gene expression, protein abundance and GO classes in the same low dimensional projections and identify GO classes that are likely to be of biological importance.

Proteomic profiling of von Hippel-Lindau syndrome and multiple endocrine neoplasia type 2 pheochromocytomas reveals different expression of chromogranin B

Pheochromocytomas are catecholamine-producing tumors that can occur in the context of von Hippel-Lindau syndrome (VHL) and multiple endocrine neoplasia type 2 (MEN2). Pheochromocytomas in these two syndromes differ in histopathological features, catecholamine metabolism, and clinical phenotype. To further investigate the nature of these differences, we compared the global protein expressions of 8 MEN2A-associated pheochromocytomas with 11 VHL-associated pheochromocytomas by two-dimensional gel electrophoresis proteomic profiling followed by sequencing and identification of differentially expressed proteins. Although both types of pheochromocytoma shared similarities in their protein expression patterns, the expression of several proteins was distinctly different between VHL- and MEN2A-associated pheochromocytomas. We identified several of these differentially expressed proteins. One of the proteins with higher expression in MEN2-associated tumors was chromogranin B, of which the differential expression was confirmed by western blot analysis. Our results expand the evidence for proteomic differences between these two tumor entities, and suggest that VHL-associated pheochromocytomas may be deficient in fundamental machinery for catecholamine storage. In light of these new findings, as well as existing evidence for differences between both types of pheochromocytomas, we propose that these tumors may have different developmental origins.