Does the serum peptidome reveal hemostatic dysregulation?

Peptidomics analysis of human blood specimens for biomarker discovery

This review addresses the concepts, limitations and perspectives for the application of peptidomics science and technologies to discover putative biomarkers in blood specimens. Peptidomics can be defined as the comprehensive multiplex analysis of endogenous peptides contained within a biological sample under defined conditions to describe the multitude of native peptides in a biological compartment. In addition to the discovery of disease associated biomarkers, an emerging field in peptidomics is the analysis of peptides to describe in vivo effects of protease inhibitors. The development and application of peptidomics technologies represent an arena of biomarker research that has the potential for adding significant clinical value.

Proteomic analysis of venous thromboembolism: an update

Venous thromboembolism is a complex, multifactorial disorder, the pathogenesis of which typically involves a variety of inherited or acquired factors. The multifactorial etiology of this disease and the partial correlation between genotype and prothrombotic phenotype limit greatly the value of genetic analysis in assessing thrombotic risk. The integration of several new 'omics' techniques enables a multifaceted and holistic approach to the study of venous thrombotic processes and pave the way to the search and identification of novel blood biomarkers and/or effectors of thrombus formation that can also be the possible future target of new anticoagulant and thrombolytic therapies for more personalized medicine. This review provides a comprehensive overview of the latest candidate proteomic biomarkers of venous thrombosis and of the proteomics studies relevant to its pathophysiology, some of which seem to confirm the existence of a common physiopathological basis for venous thromboembolism and atherothrombosis.

Specific Investigation of Sample Handling Effects on Protease Activities and Absolute Serum Concentrations of Various Putative Peptidome Cancer Biomarkers

Introduction

In the search for novel cancer biomarkers, various proteolytically derived peptides have been proposed to exhibit cancer or cancer-type specificity. As these peptides are presumably also generated after sample collection by tumor-specific proteases, extensive investigation of the involved proteolytic processes is crucial for further research.

Materials and Methods

Using two previously developed and fully validated liquid-chromatography coupled to tandem-mass spectrometry assays, absolute quantification of, in total, 13 proteolytically derived peptides in human serum was accomplished. The analytes included eight peptides derived from inter-α-trypsin inhibitor heavy chain-4 (ITIH₄-30, ITIH₄-29, ITIH₄-28, ITIH₄-27, ITIH₄-26, ITIH₄-25, ITIH₄-22, and ITIH₄-21), bradykinin, des-Arg⁹-bradykinin, Hyp³-bradykinin, and fragments from fibrinogen-α-chain (Fib-α _[605–629]) and complement component 4a (C4a _{[1337–1350]}). Samples were obtained from different healthy individuals and prepared with variable tube types, clotting times, and temperatures. Furthermore, stabilities in the serum fraction were assessed and compared to stabilities in serum from breast cancer patients.

Results and Discussion

The quantitative analyses showed either increasing or decreasing serum concentrations during blood coagulation, while comparable effects were observed in serum separated from the blood clot. Furthermore, comparisons of inter- and intra-individual variations suggested better reflection of an individual’s protease activity after prolonged ex vivo incubation. This was illustrated for the putative breast cancer marker ITIH₄-22, revealing better differentiation after incubation of serum at ambient temperature for 24 h.

Conclusion

The presented study provides suggestions for more specific and optimized sample preparation, as well as extended knowledge necessary to further explore the opportunities of these proteolytic peptides as cancer biomarkers.

Using the protein chip interface with quadrupole time-of-flight mass spectrometry to directly identify peaks in SELDI profiles--initial evaluation using low molecular weight serum peaks

Mass spectrometric profiling, particularly in the form of SELDI, has been used in many studies, particularly in attempts to generate diagnostic serum profiles. Several studies have generated promising results but one of the limitations is the inability to identify easily potential discriminatory peaks. This may enable specific assays to be developed and increased biological insight. We describe the first systematic technical evaluation of the ProteinChip interface coupled to a tandem mass spectrometer which allows direct sequencing of peptides <6000 Da, and describe the direct sequence identification of 21 peaks commonly observed in serum samples. Additionally we describe for the first time the use of on-chip acetylation to assist in the validation of sequence identification.

Proteomics-driven cancer biomarker discovery: looking to the future

Availability of a suite of biomarkers for early detection, stratification into distinct subtypes, and monitoring progression or response to therapy promises significant improvements in clinical outcomes for cancer patients. However, despite the recent progress in proteomics technologies based on mass spectrometry (MS), discovery of novel clinical assessment tools has been slow. This is, partly due to the inherent difficulties in working with blood as the biospecimen for candidate discovery. A better understanding of the limitations of blood for comparative protein profiling and a better appreciation of the advantages of cancer tissue or cancer cell secretomes have the potential to greatly enhance the progress.

Cryptides: buried secrets in proteins

The proteome originally described the entire set of proteins expressed by a genome, tissue or organism. Subsequently this term was limited to all the expressed proteins at a given time under defined conditions. Hence, specializations such as functional proteome, cancer proteome, liver proteome and so forth have arisen. One particular proteome that has been recently described is the cryptome, a unique subset of already known proteins that has the ability of generating bioactive peptides and proteins when submitted to proteolytic cleavage, rather than the classical processing pathways. This is an idea in agreement with the concept that evolution is not related to the amount of genes or putative proteins that could be secreted by an organism, but to the way these proteins are processed. These 'new' molecules may have related or increased properties when compared to the 'original' molecule or possess completely unrelated biological effects, thus increasing the array of biological roles that can be associated to one given protein (or gene). In this work, we review this recent concept and put it into the toxinology field as well, an area in which the diversity of functional molecules (and roles) is essential for the survival of a given organism.

Cancer biomarker discovery via low molecular weight serum proteome profiling - Where is the tumor?

Time-course analyses of rapidly processed serum performed in parallel by SELDI and nanoscale LC-MS/MS have revealed the temporal correlation of several literature-based disease markers with ex vivo driven events such that their in vivo existence in healthy subjects is questionable. Identification by MS/MS reveals these putative biomarkers to be byproducts of the coagulation cascade and platelet activation and suggests plasmatic analysis may be preferred. In a pilot plasmatic study, a cohort of naïve prostate cancer (PCa) samples were uniformly distinguished from their age-matched controls (n = 20) on the basis of multiple peptidic components; most notably by a derivative of complement C(4) at 1863 m/z (GLEEELQFSLGSKINVK, C4(1353-1369) ). The fully tryptic nature of this and other putative PCa discriminants is consistent with the cleavage specificity of common blood proteases and questions the need for tumor-derived proteolytic activities as has been proposed. In light of the known correlation of disregulated hemostasis with malignant disease, we suggest the underlying differentiating phenomena in these types of analyses may lie in the temporal disparity of sample activation such that the case (patient) samples are preactivated while the control samples are not.