The utility of isotope-coded protein labeling for prioritization of proteins found in ovarian cancer patient urine

An effective urobilin clearance strategy based on paramagnetic beads facilitates microscale proteomic analysis of urine

Urine provides an ideal source for disease biomarker discovery. High-adhesion contaminants such as urobilin, which are difficult to remove from urine, can severely interfere with urinary proteomic analysis. Here, we aimed to establish a strategy based on single-pot, solid-phase-enhanced sample preparation (SP3) technology to prepare samples for urinary proteomics analysis that almost completely eliminates the impact of urobilin. A systematic evaluation of the effects of two urinary protein precipitation methods, two types of protein lysis buffers, and different ratios of magnetic digestion beads on the identification and quantification of the microscale urinary proteome was conducted. Our results indicate that methanol-chloroform precipitation, coupled with efficient lysis facilitated by urea, and subsequent enzymatic digestion using a mix of hydrophilic and hydrophobic magnetic beads offers the best performance. Further applying this strategy to the urine of patients with benign prostatic hyperplasia, prostate cancer and healthy individuals, combined with a narrow window of data-independent acquisition, FGFR4, MYLK, ORM2, GOLM1, SPP1, CD55, CSF1, DLD and TIMP3 were identified as potential biomarkers to discriminate benign prostatic hyperplasia and prostate cancer patients.

Recent progress in mass spectrometry-based urinary proteomics

Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.

MALDI-TOF/MS Analysis of Non-Invasive Human Urine and Saliva Samples for the Identification of New Cancer Biomarkers

Cancer represents a group of heterogeneous diseases that are a leading global cause of death. Even though mortality has decreased in the past thirty years for different reasons, most patients are still diagnosed at the advanced stage, with limited therapeutic choices and poor outcomes. Moreover, the majority of cancers are detected using invasive painful methods, such as endoscopic biopsy, making the development of non-invasive or minimally invasive methods for the discovery and fast detection of specific biomarkers a crucial need. Among body fluids, a valuable non-invasive alternative to tissue biopsy, the most accessible and least invasive are undoubtedly urine and saliva. They are easily retrievable complex fluids containing a large variety of endogenous compounds that may provide information on the physiological condition of the body. The combined analysis of these fluids with matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF/MS), a reliable and easy-to-use instrumentation that provides information with relatively simple sample pretreatments, could represent the ideal option to rapidly achieve fast early stage diagnosis of tumors and their real-time monitoring. On this basis, the present review summarizes the recently reported applications relevant to the MALDI analysis of human urine and saliva samples.

Keratin-14 (KRT14) Positive Leader Cells Mediate Mesothelial Clearance and Invasion by Ovarian Cancer Cells

Epithelial ovarian cancer metastasis is driven by spheroids, which are heterogeneous cancer cell aggregates released from the primary tumour mass that passively disseminate throughout the peritoneal cavity to promote tumour spread, disease recurrence, and acquired chemoresistance. Despite their clinical importance, the molecular events that control spheroid attachment and invasion into underlying healthy tissues remain poorly understood. We examined a novel in vitro invasion model using imaging mass spectrometry to establish a “snapshot” of the spheroid/mesothelial interface. Amongst numerous adhesion-related proteins, we identified a sub-population of highly motile, invasive cells that expressed the basal epithelial marker KRT14 as an absolute determinant of invasive potential. The loss of KRT14 completely abrogated the invasive capacity, but had no impact on cell viability or proliferation, suggesting an invasion-specific role. Our data demonstrate KRT14 cells as an ovarian cancer “leader cell” phenotype underlying tumor invasion, and suggest their importance as a clinically relevant target in directed anti-tumour therapies.

Preparation of a thickness-controlled Mg-MOFs-based magnetic graphene composite as a novel hydrophilic matrix for the effective identification of the glycopeptide in the human urine

The highly effective analysis of glycopeptides from complex biological samples is an attractive and critical topic all the time. In this study, a novel thickness-controlled hydrophilic Mg-metal organic frameworks (Mg-MOFs) coating-functionalized magnetic graphene composite (MagG@Mg-MOFs-1C) was prepared for the capture of the glycopeptides. The as-synthesized composite exhibits an ultralow limit of detection (0.1 fmol μL-1), a perfect size-exclusion effect (HRP digests/BSA protein/HRP protein, 1 : 500 : 500, w/w/w), and a high binding capacity (150 mg g-1), satisfying reusability and high recovery in the recognition of glycopeptides due to its outstanding characteristics including strong magnetic property, large surface area (617 m2 g-1), plenty of affinity sites, and excellent hydrophilicity. Furthermore, the MagG@Mg-MOFs-1C composite was successfully applied to selectively enriched glycopeptides in human urine. More excitingly, 406 N-glycosylation peptides corresponding to 185 glycoproteins were identified in the urine of the bladder cancer patients, in which these identified glycoproteins include the potential biomarkers (α-2-macroglobulin, complement C4-B, and α-1-antitrypsin) for the bladder cancer. This study suggests that the hydrophilic porous MOFs-functionalized composite has a great potential in the large-scale characterization of the low-abundance biomolecules in urine, opening a new avenue for the rapid and convenient diagnosis of the disease.

Relative and Absolute Quantitation in Mass Spectrometry-Based Proteomics

Mass spectrometry-based quantitative proteomics is a powerful tool for gaining insights into function and dynamics of biological systems. However, peptides with different sequences have different ionization efficiencies, and their intensities in a mass spectrum are not correlated with their abundances. Therefore, various label-free or stable isotope label-based quantitation methods have emerged to assist mass spectrometry to perform comparative proteomic experiments, thus enabling nonbiased identification of thousands of proteins differentially expressed in healthy versus diseased cells. Here, we discuss the most widely used label-free and metabolic-, enzymatic-, and chemical labeling-based proteomic strategies for relative and absolute quantitation. We summarize the specific strengths and weaknesses of each technique in terms of quantification accuracy, proteome coverage, multiplexing capability, and robustness. Applications of each strategy for solving specific biological complexities are also presented.

Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences

Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (³ H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.

Autoantibodies against HSF1 and CCDC155 as Biomarkers of Early-Stage, High-Grade Serous Ovarian Cancer

Background: Tumor-directed circulating autoantibodies (AAb) are a well-established feature of many solid tumor types, and are often observed prior to clinical disease manifestation. As such, they may provide a good indicator of early disease development. We have conducted a pilot study to identify novel AAbs as markers of early-stage HGSOCs.Methods: A rare cohort of patients with early (FIGO stage Ia-c) HGSOCs for IgG, IgA, and IgM-mediated AAb reactivity using high-content protein arrays (containing 9,184 individual proteins). AAb reactivity against selected antigens was validated by ELISA in a second, independent cohort of individual patients.Results: A total of 184 antigens were differentially detected in early-stage HGSOC patients compared with all other patient groups assessed. Among the six most highly detected "early-stage" antigens, anti-IgA AAbs against HSF1 and anti-IgG AAbs CCDC155 (KASH5; nesprin 5) were significantly elevated in patients with early-stage malignancy. Receiver operating characteristic (ROC) analysis suggested that AAbs against HSF1 provided better detection of early-stage malignancy than CA125 alone. Combined measurement of anti-HSF1, anti-CCDC155, and CA125 also improved efficacy at higher sensitivity.Conclusions: The combined measurement of anti-HSF1, anti-CCDC155, and CA125 may be useful for early-stage HGSOC detection.Impact: This is the first study to specifically identify AAbs associated with early-stage HGSOC. The presence and high frequency of specific AAbs in early-stage cancer patients warrants a larger scale examination to define their value for early disease detection at primary diagnosis and/or recurrence. Cancer Epidemiol Biomarkers Prev; 27(2); 183-92. ©2017 AACR.

The comparison of CHCA solvent compositions for improving LC-MALDI performance and its application to study the impact of aflatoxin B1 on the liver proteome of diabetes mellitus type 1 mice

In nanoflow liquid chromatography-matrix-assisted laser desorption/ionization tandem time-of-flight (nanoLC-MALDI-TOF/TOF) approaches, it is critical to directly apply small amounts of the sample elutes on the sample target using a nanoLC system due to its low flow rate of 200 ~ 300 nl/min. It is recommended to apply a sheath liquid containing a matrix with a several μL/min flow rate at the end of the nanoLC column to ensure a larger co-eluted droplet for more reproducible sample spotting and avoid the laborious task of post-manual matrix spotting. In this study, to achieve a better nanoLC-MALDI performance on sample spotting, we first compared α-Cyano-4-hydroxycinnamic acid (CHCA) solvent composition for efficiently concentrating nanoLC elutes on an anchor chip. The solvent composition of isopropanol (IPA): acetonitrile (ACN):acetone:0.1% Trifluoroacetic acid (TFA) (2:7:7:2) provided strong and homogeneous signals with higher peptide ion yields than the other solvent compositions. Then, nanoLC-MALDI-TOF/TOF was applied to study the impact of aflatoxin B1 on the liver proteome from diabetes mellitus type 1 mice. Aflatoxin B1 (AFB1), produced by Aspergillus flavus and Aspergillus parasiticus is a carcinogen and a known causative agent of liver cancer. To evaluate the effects of long-term exposure to AFB1 on type 1 diabetes mellitus (TIDM), the livers of T1DM control mice and mice treated with AFB1 were analyzed using isotope-coded protein labeling (ICPL)-based quantitative proteomics. Our results showed that gluconeogenesis, lipid, and oxidative phosphorylation mechanisms, normally elevated in T1DM, were disordered following AFB1 treatment. In addition, major urinary protein 1 (MUP1), an indicator of increased insulin sensitivity, was significantly decreased in the T1DM/AFB1 group and may have resulted in higher blood glucose levels compared to the T1DM group. These results indicate that T1DM patients should avoid the AFB1 intake, as they could lead to increased blood glucose levels and disorders of energy-producing mechanisms.

Effects of arginine vasopressin on the urine proteome in rats

Biomarkers are the measurable changes associated with a physiological or pathophysiological process. The content of urine frequently changes because it is not controlled by homeostatic mechanisms, and these alterations can be a source of biomarkers. However, urine is affected by many factors. In this study, vasoconstrictor and antidiuretic arginine vasopressin (AVP) were infused into rats using an osmotic pump. The rats’ urinary proteome after one week of infusion was analyzed by label-free LC-MS/MS. A total of 408 proteins were identified; among these proteins, eight and 10 proteins had significantly altered expression in the low and high dose groups, respectively, compared with the control group using the one-way ANOVA analysis followed by post hoc analysis with the least significant difference (LSD) test or Dunnett’s T3 test. Three differential proteins were described in prior studies as related to AVP physiological processes, and nine differential proteins are known disease biomarkers. Sixteen of the 17 differential proteins have human orthologs. These results suggest that we should consider the effects of AVP on urinary proteins in future urinary disease biomarker researches. The study data provide clues regarding underlying mechanisms associated with AVP for future physiological researches on AVP. This study provide a sensitive changes associated with AVP. However, the limitation of this result is that the candidate biomarkers should be further verified and filtered. Large clinical samples must be examined to verify the differential proteins identified in this study before these proteins are used as biomarkers for pathological AVP increased diseases, such as syndrome of inappropriate antidiuretic hormone secretion (SIADH).

HE4-test of urine and body fluids for diagnosis of gynecologic cancer

Serum epididymis protein 4 (HE4) level is a useful biomarker for the management of ovarian and endometrial cancer patients. Urine HE4-test, with its easier access than serum test, has emerged as a new method with promising application for the diagnosis of ovarian cancer. Areas covered: This review summarizes data regarding the detection and alteration of HE4 in urine samples collected from ovarian cancer patients and controls. The performance and limitation of the assay and potential direction of future study are also discussed. Expert commentary: Several studies have demonstrated an appreciable efficiency of urine HE4-test in the discrimination of ovarian cancer patients from general population. However, the data is based on small cohorts, and the performance of urine HE4-test need to be validated in larger groups. An algorithm incorporating other important factors may allow a quantitative assessment of cancer possibility. Future studies on the HE4 renal secretion and HE4 degradation dynamics in urine are also required for the establishment of standard protocols for the application of urine HE4-test in clinical settings.

Accurate quantification of modified cyclic peptides without the need for authentic standards

There is a growing interest in the use of cyclic peptides as therapeutics, but their efficient production is often the bottleneck in taking them forward in the development pipeline. We have recently developed a method to synthesise azole-containing cyclic peptides using enzymes derived from different cyanobactin biosynthetic pathways. Accurate quantification is crucial for calculation of the reaction yield and for the downstream biological testing of the products. In this study, we demonstrate the development and validation of two methods to accurately quantify these compounds in the reaction mixture and after purification. The first method involves the use of a HPLC coupled in parallel to an ESMS and an ICPMS, hence correlating the calculated sulfur content to the amount of cyclic peptide. The second method is an NMR ERETIC method for quantifying the solution concentration of cyclic peptides. These methods make the quantification of new compounds much easier as there is no need for the use of authentic standards when they are not available.

Identification of novel dipeptidyl peptidase 9 substrates by two-dimensional differential in-gel electrophoresis

Dipeptidyl peptidase 9 (DPP9) is a member of the S9B/DPPIV (DPP4) serine protease family, which cleaves N-terminal dipeptides at an Xaa-Pro consensus motif. Cytoplasmic DPP9 has roles in epidermal growth factor signalling and in antigen processing, whilst the role of the recently discovered nuclear form of DPP9 is unknown. Mice lacking DPP9 proteolytic activity die as neonates. We applied a modified 2D differential in-gel electrophoresis approach to identify novel DPP9 substrates, using mouse embryonic fibroblasts lacking endogenous DPP9 activity. A total of 111 potential new DPP9 substrates were identified, with nine proteins/peptides confirmed as DPP9 substrates by MALDI-TOF or immunoblotting. Moreover, we also identified the dipeptide Val-Ala as a consensus site for DPP9 cleavage that was not recognized by DPP8, suggesting different in vivo roles for these closely related enzymes. The relative kinetics for the cleavage of these nine candidate substrates by DPP9, DPP8 and DPP4 were determined. This is the first identification of DPP9 substrates from cells lacking endogenous DPP9 activity. These data greatly expand the potential roles of DPP9 and suggest different in vivo roles for DPP9 and DPP8.

Stable isotope labelling methods in mass spectrometry-based quantitative proteomics

Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons.