Peptidomics of Urine and Other Biofluids for Cancer Diagnostics

Sample-dependent diagnostic accuracy of prostaglandin D synthase in cerebrospinal fluid leak

BACKGROUND

Prostaglandin D2 synthase, commonly known as β-trace protein (βTP), is an excellent biomarker for the assessment of cerebrospinal fluid (CSF) leaks. Despite being widely used, the limits for the diagnostic values of βTP are not well established to date, and currently suggested cut-off values in literature range from 0.25 to 6.0mg/L. Sample-specific and more accurate thresholds are a current need.

METHODS

A retrospective observational study, performed in a tertiary-care hospital, between January 2006 and January 2014. A total of 74 patients were included, with a definitive diagnosis after initial leak suspicion and at least one determination of βTP using a nephelometry-based assay. A total of 46 CSF samples were included in the control group. Samples were obtained from nasal secretions, ear secretions or spinal surgical injury, directly using sterile Eppendorf tubes. The analysis of 3 different cut-off values was performed and the receiver operating curve (ROC) analyses were calculated.

RESULTS

Initial diagnostic suspicion was confirmed in 51% of cases, most of which were of postoperative origin (51%) and traumatic (26%). The βTP median concentration in different samples was significantly higher in the presence of cerebrospinal fluid fistula, regardless of sample type (22.0mg/L vs. 0.24mg/L, 95% confidence interval: 19.0-30.8 vs. 0.08-0.40; p<0.001). Data from contingency tables show 100% sensitivity and specificity, depending on sample type and the cut-off value used: for rhinorrhea and otorrhea samples, the most appropriate it was 0.7mg/L, while values >2.0mg/L could be used for spine postoperative fluid leakage samples.

CONCLUSIONS

The cut off value for βTP in the diagnosis and follow-up of cerebrospinal fluid leaks should be modified depending on the type of secretion (sample type), for a better diagnostic accuracy.

Proteomics and peptidomics: moving toward precision medicine in urological malignancies

Urological malignancies are a major cause of morbidity and mortality worldwide. Advances in early detection, diagnosis, prognosis and prediction of treatment response can significantly improve patient care. Proteomic and peptidomic profiling studies are at the center of kidney, prostate and bladder cancer biomarker discovery and have shown great promise for improved clinical assessment. Mass spectrometry (MS) is the most widely employed method for proteomic and peptidomic analyses. A number of MS platforms have been developed to facilitate accurate identification of clinically relevant markers in various complex biological samples including tissue, urine and blood. Furthermore, protein profiling studies have been instrumental in the successful introduction of several diagnostic multimarker tests into the clinic. In this review, we will provide a brief overview of high-throughput technologies for protein and peptide based biomarker discovery. We will also examine the current state of kidney, prostate and bladder cancer biomarker research as well as review the journey toward successful clinical implementation.

LRG1 downregulation in allergic airway disorders and its expression in peripheral blood and tissue cells

Background

Increased leucine-rich α2-glycoprotein-1 (LRG1) has been observed in plasma of individuals with various diseases. However, the role of LRG1 in allergic airway disease has not been investigated.

Objective

To explore the involvement of LRG1 in allergy and its cell origins.

Methods

The expression levels of LRG1 and its receptor transforming growth factor-beta receptor II (TGFBR2) in patients with allergic rhinitis (AR) and asthma (AS) were examined by flow cytometry, and enzyme-linked immunosorbent assay (ELISA).

Results

LRG1 and soluble TGFBR2 expression in plasma of patients with AR and AS were markedly lower than that of healthy control (HC) subjects. Large proportions of CD123 + HLA-DR−, CD16+, CD4+, CD8+, CD14+, and CD19+ cells expressed LRG1, although the percentages of LRG1+ cells in these cell populations were lower in AR and AS patients. Up to 89.8 and 15.5 % of dispersed mast cells expressed LRG1 and TGFBR2. Moreover, allergen extract exposure significantly reduced LRG1 and TGFBR2 expression in the plasma and leukocytes of patients with AR and AS.

Conclusions

Reduced LRG1 and TGFBR2 levels in patients with allergic airway disorders are likely caused by inhibitory actions of allergens in LRG1 producing cells. Thus, LRG1 may be a key regulatory factor of allergic responses.

Noninvasive strategies for breast cancer early detection

Breast cancer screening and presurgical diagnosis are currently based on mammography, ultrasound and more sensitive imaging technologies; however, noninvasive biomarkers represent both a challenge and an opportunity for early detection of cancer. An extensive number of potential breast cancer biomarkers have been discovered by microarray hybridization or sequencing of circulating DNA, noncoding RNA and blood cell RNA; multiplex analysis of immune-related molecules and mass spectrometry-based approaches for high-throughput detection of protein, endogenous peptides, circulating and volatile metabolites. However, their medical relevance and their translation to clinics remain to be exploited. Once they will be fully validated, cancer biomarkers, used in combination with the current and emerging imaging technologies, represent an avenue to a personalized breast cancer diagnosis.

Mining the Human Proteome: Biomarker Discovery for Human Cancer and Metastases

As our knowledge of the mechanisms underlying cancer development and progression has increased, so too have more effective, less toxic, and targeted therapies begun to reach the clinic. However, the full impact of these clinical advances and the practical success of the emerging field of precision medicine are dependent on the discovery and validation of sensitive and accurate biomarkers that can enable appropriate and rigorous sample type and patient selection, reliable longitudinal monitoring of therapeutic efficacy, and even risk assessment and early detection. Within the context of this review, we examine state-of-the-art approaches to the discovery and validation of noninvasive cancer biomarkers, with a specific emphasis on those that are protein or protein-associated ones. We also review sample selection strategies, currently utilized proteomic approaches for both discovery and validation requirements, and data analysis standards. Finally, we provide examples of these elements of biomarker discovery and validation from our own biomarker research.

Graphene-Templated Synthesis of Magnetic Metal Organic Framework Nanocomposites for Selective Enrichment of Biomolecules

Successful control of homogeneous and complete coating of graphene or graphene-based composites with well-defined metal organic framework (MOF) layers is a great challenge. Herein, novel magnetic graphene MOF composites were constructed via a simple strategy for self-assembly of well-distributed, dense, and highly porous MOFs on both sides of graphene nanosheets. Graphene functionalized with magnetic nanoparticles and carboxylic groups on both sides was explored as the backbone and template to direct the controllable self-assembly of MOFs. The prepared composite materials have a relatively high specific surface area (345.4 m(2) g(-1)), and their average pore size is measured to be 3.2 nm. Their relatively high saturation magnetization (23.8 emu g(-1)) indicates their strong magnetism at room temperature. Moreover, the multifunctional composite was demonstrated to be a highly effective affinity material in selective extraction and separation of low-concentration biomolecules from biological samples, in virtue of the size-selection property of the unique porous structure and the excellent affinity of the composite materials. Besides providing a solution for the construction of well-defined functional graphene-based MOFs, this work could also contribute to selective extraction of biomolecules, in virtue of the universal affinity between immobilized metal ions and biomolecules.

Tissue Factor: A Conventional or Alternative Target in Cancer Therapy

BACKGROUND

Tissue factor (TF) is an evolutionary conserved glycoprotein that plays an important role in the pathogenesis of cancer. TF is expressed in 2 naturally occurring protein isoforms, membrane-bound full-length (fl)TF and soluble alternatively spliced (as)TF. Both isoforms have been shown to affect a variety of pathophysiologically relevant functions, such as tumor-associated angiogenesis, thrombogenicity, tumor growth, and metastasis. Therefore, targeting TF either by direct inhibition or indirectly, i.e., on a posttranscriptional level, offers a novel therapeutic option for cancer treatment.

CONTENT

In this review we summarize the latest findings regarding the role of TF and its isoforms in cancer biology. Moreover, we briefly depict and discuss the therapeutic potential of direct and/or indirect inhibition of TF activity and expression for the treatment of cancer.

SUMMARY

asTF and flTF play important and often distinct roles in cancer biology, i.e., in thrombogenicity and angiogenesis, which is mediated by isoform-specific signal transduction pathways. Therefore, both TF isoforms and downstream signaling are promising novel therapeutic targets in malignant diseases.

Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases

Background

Assays of molecular biomarkers in urine are non-invasive compared to other body fluids and can be easily repeated. Based on the hypothesis that the secreted markers from the diseased organs may locally release into the body fluid in the vicinity of the injury, urine-based assays have been considered beneficial to monitoring bladder health and urological diseases. The urine proteome is much less complex than the serum and tissues, but nevertheless can contain biomarkers for diagnosis and prognosis of diseases. The urine metabolome has a much higher number and concentration of low-molecular metabolites than the serum or tissues, with a far lower lipid concentration, yet informs directly about dietary and microbial metabolism.

Discussion

We here discuss the use of mass spectrometry-based proteomics and metabolomics for urine biomarker assays, specifically with respect to the underlying mechanisms that trigger the pathological condition.

Conclusion

Molecular biomarker profiles, based on proteomics and metabolomics studies, reliably distinguish patients from healthy controls, stratify sub-populations with respect to treatment options, and predict therapeutic response of patients with urological disease.

Deciphering the complexity of the cancer proteome for diagnostic applications

The proteome is the most functional component encoded in the genome, yet most features of the proteome that are deregulated in cancer cannot be predicted from genomic analysis alone. These include post-translational modifications (PTMs), sub-cellular localization, networks and circuitry, formation of complexes, and functional activity, all of which could play a role or be affected as part of tumorigenesis. Thus, there is a substantial opportunity to elucidate protein alterations in cancer and to translate knowledge into diagnostics and therapeutics. The progress made in mining the cancer proteome for diagnostic applications and the path forward are herein reviewed.

Peptidomics for the discovery and characterization of neuropeptides and hormones

The discovery of neuropeptides as signaling molecules with paracrine or hormonal regulatory functions has led to trailblazing advances in physiology and fostered the characterization of numerous neuropeptide-binding G protein-coupled receptors (GPCRs) as potential drug targets. The impact on human health has been tremendous: approximately 30% of commercial drugs act via the GPCR pathway. However, about 25% of the GPCRs encoded by the mammalian genome still lack their pharmacological identity. Searching for the orphan GPCR endogenous ligands that are likely to be neuropeptides has proved to be a formidable task. Here we describe the mass spectrometry (MS)-based technologies and experimental strategies that have been successful in achieving high-throughput characterization of endogenous peptides in nervous and endocrine systems.

Is isolation of comprehensive human plasma peptidomes an achievable quest?

The low molecular weight (LMW; <10kDa)* plasma peptidome has been considered a source of useful diagnostic biomarkers and potentially therapeutic molecules, as it contains many cytokines, peptide hormones, endogenous peptide products and potentially bioactive fragments derived from the parent proteome. The small size of the peptides allows them almost unrestricted vascular and interstitial access, and hence distribution across blood-brain barriers, tumour and other vascular permeability barriers. Therefore, the peptidome may carry specific signatures or fingerprints of an individual's health, wellbeing or disease status. This occurs primarily because of the advantage the peptidome has in being readily accessible in human blood and/or other biofluids. However, the co-expression of highly abundant proteins (>10kDa) and other factors present inherently in human plasma make direct analysis of the blood peptidome one of the most challenging tasks faced in contemporary analytical biochemistry. A comprehensive compendium of extraction and fractionation tools has been collected concerning the isolation and micromanipulation of peptides. However, the search for a reliable, accurate and reproducible single or combinatorial separation process for capturing and analysing the plasma peptidome remains a challenge. This review outlines current techniques used for the separation and detection of plasma peptides and suggests potential avenues for future investigation. This article is part of a Special Issue entitled: HUPO 2014.