Low-molecular weight plasma proteome analysis using centrifugal ultrafiltration

Neuronal internalization of immunoglobulin G injected into the mouse brain by a novel absorption strategy to avoid unwanted interaction with immune complex using centrifugal filtration

Monoclonal immunoglobulin-G (IgG) antibodies are now emerging as therapeutic tools to tackle various disorders, including those affecting the brain. However, little is known about how these IgG molecules behave in the brain. To better understand the potential behavior of IgG molecules in the brain, here we established a specific protocol to immunolocalize rat IgG injected into mouse striatum with an anti-rat IgG antibody. Using double immunolabeling, IgG-like immunoreactivity (IR) was mainly found in neurons but scarcely observed in glia 1 h after intrastriatal injection of IgG, whereas some surrounding glia contained IgG-like IR 24 h after injection. However, preabsorption with a large excess of rat IgG to confirm the authenticity of this labeling failed to eliminate this neuronal IgG-like IR but rather exhibited nuclear staining in glial cells. Because this unexpected nuclear staining escalated with increasing amount of absorbing IgG, we postulated that this nuclear staining is due to formation of immune complex IgG-anti-IgG, which can be removed by centrifugal filtration. As expected, this nuclear staining in glial cells was eliminated after centrifugal filtration of the IgG/anti-IgG mixture, and authentic IgG-like IR was chiefly detected in the cytoplasm of neurons around the injection channel. This study is the first demonstration of neuronal redistribution of injected IgG in the mouse brain. Neuronal internalization of exogenous IgG may be advantageous especially when the therapeutic targets of monoclonal IgG are intraneuronal such as neurofibrillary tangles or Lewy bodies.

Advances in biomarker detection: Alternative approaches for blood-based biomarker detection

In the clinical setting, a blood sample is typically the starting point for biomarker search and discovery. Mass spectrometry (MS) is a highly sensitive and informative method for characterizing a very wide range of metabolites and proteins and is therefore a potentially powerful tool for biomarker discovery. However, the physicochemical characteristics of blood coupled with very large ranges of protein and metabolite concentrations present a significant technical obstacle for resolving and quantifying putative biomarkers by MS. Blood fractionation procedures are being developed to reduce the proteome/metabolome complexity and concentration ranges, allowing a greater diversity of analytes, including those at very low concentrations, to be quantified. In this chapter, several strategies for enriching and/or isolating specific blood components are summarized, including methods for the analysis of low and high molecular weight compounds, usually neglected in this type of assays, extracellular vesicles, and peripheral blood mononuclear cells (PBMCs). For each method, relevant practical information is presented for effective implementation.

Analysis of bodily fluids using vibrational spectroscopy: a direct comparison of Raman scattering and infrared absorption techniques for the case of glucose in blood serum

Analysis of biomarkers present in the blood stream can potentially deliver crucial information on patient health and indicate the presence of numerous pathologies.

Direct Assessment of Plasma/Serum Sample Quality for Proteomics Biomarker Investigation

Blood proteome analysis for biomarker discovery represents one of the most challenging tasks to be achieved through clinical proteomics due to the sample complexity, such as the extreme heterogeneity of proteins in very dynamic concentrations, and to the observation of proper sampling and storage conditions. Quantitative and qualitative proteomics profiling of plasma and serum could be useful both for the early detection of diseases and for the evaluation of pathological status. Two main sources of variability can affect the precision and accuracy of the quantitative experiments designed for biomarker discovery and validation. These sources are divided into two categories, pre-analytical and analytical, and are often ignored; however, they can contribute to consistent errors and misunderstanding in biomarker research. In this chapter, we review critical pre-analytical and analytical variables that can influence quantitative proteomics. According to guidelines accepted by proteomics community, we propose some recommendations and strategies for a proper proteomics analysis addressed to biomarker studies.

The Peptidome Comes of Age: Mass Spectrometry-Based Characterization of the Circulating Cancer Peptidome

Peptides play a seminal role in most physiological processes acting as neurotransmitters, hormones, antibiotics, and immune regulation. In the context of tumor biology, it is hypothesized that endogenous peptides, hormones, cytokines, growth factors, and aberrant degradation of select protein networks (e.g., enzymatic activities, protein shedding, and extracellular matrix remodeling) are fundamental in mediating cancer progression. Analysis of peptides in biological fluids by mass spectrometry holds promise of providing sensitive and specific diagnostic and prognostic information for cancer and other diseases. The identification of circulating peptides in the context of disease constitutes a hitherto source of new clinical biomarkers. The field of peptidomics can be defined as the identification and comprehensive analysis of physiological and pathological peptides. Like proteomics, peptidomics has been advanced by the development of new separation strategies, analytical detection methods such as mass spectrometry, and bioinformatic technologies. Unlike proteomics, peptidomics is targeted toward identifying endogenous protein and peptide fragments, defining proteolytic enzyme substrate specificity, as well as protease cleavage recognition (degradome). Peptidomics employs "top-down proteomics" strategies where mass spectrometry is applied at the proteoform level to analyze intact proteins and large endogenous peptide fragments. With recent advances in prefractionation workflows for separating peptides, mass spectrometry instrumentation, and informatics, peptidomics is an important field that promises to impact on translational medicine. This review covers the current advances in peptidomics, including top-down and imaging mass spectrometry, comprehensive quantitative peptidome analyses (developments in reproducibility and coverage), peptide prefractionation and enrichment workflows, peptidomic data analyses, and informatic tools. The application of peptidomics in cancer biomarker discovery will be discussed.

A protocol for exosome isolation and characterization: evaluation of ultracentrifugation, density-gradient separation, and immunoaffinity capture methods

Exosomes are 40-150 nm extracellular vesicles that are released from a multitude of cell types, and perform diverse cellular functions including intercellular communication, antigen presentation, and transfer of tumorigenic proteins, mRNA and miRNA. Exosomes are important regulators of the cellular niche, and their altered characteristics in many diseases, such as cancer, suggest their importance for diagnostic and therapeutic applications, and as drug delivery vehicles. Exosomes have been purified from biological fluids and in vitro cell cultures using a variety of strategies and techniques. In this chapter, we reveal the protocol and key insights into the isolation, purification and characterization of exosomes, distinct from shed microvesicles and apoptotic blebs. Using the colorectal cancer cell line LIM1863 as a cell model, a comprehensive evaluation of exosome isolation methods including ultracentrifugation (UC-Exos), OptiPrep™ density-based separation (DG-Exos), and immunoaffinity capture using anti-EpCAM-coated magnetic beads (IAC-Exos) were examined. All exosome isolation methodologies contained 40-150 nm vesicles based on electron microscopy, and positive for exosome markers (Alix, TSG101, HSP70) based on immunoblotting. This protocol employed a proteomic profiling approach to characterize the protein composition of exosomes, and label-free spectral counting to evaluate the effectiveness of each method in exosome isolation. Based on the number of MS/MS spectra identified for exosome markers and proteins associated with their biogenesis, trafficking, and release, IAC-Exos was shown to be the most effective method to isolate exosomes. However, the use of density-based separation (DG-Exos) provides significant advantages for exosome isolation when the use of immunoaffinity capture is limited (due to antibody availability and suitability of exosome markers).

Depletion of abundant plasma proteins by poly(N-isopropylacrylamide-acrylic acid) hydrogel particles

Protein and proteome analysis of human blood plasma presents a challenge to current analytical platforms such as mass spectrometry (MS). High abundance plasma proteins interfere with detection of potential protein biomarkers that are often 3-10 orders of magnitude lower in concentration. We report the application of pH-sensitive poly(N-isopropylacrylamide-acrylic acid) hydrogel particles for removal of abundant plasma proteins, prior to proteome analysis by MS. Protein depletion occurs by two separate mechanisms: (1) hydrogel particles incubated with low concentrations of plasma capture abundant proteins at higher efficiency than low abundance proteins, which are enriched in the supernatants, whereas (2) hydrogel particles incubated with high concentrations of plasma capture and irreversibly trap abundant proteins. During the elution step, irreversibly trapped proteins remain captured while low abundance proteins are released and recovered in the eluate. We developed a series of distinct depletion protocols that proved useful for sample depletion and fractionation and facilitated targeted analysis of putative biomarkers such as IGF1-2, IBP2-7, ALS, KLK6-7, ISK5, and PLF4 by selected reaction monitoring (SRM) liquid chromatography (LC)-MS/MS. This novel use of hydrogel particles opens new perspectives for biomarker analysis based on mass spectrometry.

Investigation and reduction of sub-microgram peptide loss using molecular weight cut-off fractionation prior to mass spectrometric analysis

This work investigates the introduction of methanol and a salt modifier to molecular weight cut-off membrane-based centrifugal filters (MWCO) to enrich sub-microgram peptide quantities. Using a neuropeptide standard, bradykinin, sample loss was reduced over two orders of magnitude with and without undigested protein present. Additionally, a bovine serum albumin tryptic digestion was investigated. Twenty-seven tryptic peptides were identified from MALDI mass spectra after enriching with methanol while only two tryptic peptides were identified after MWCO separation using H(2)O. The strategy presented here enhances recovery from MWCO separation for sub-µg peptide samples.

Separation of plasmid DNA isoforms using centrifugal ultrafiltration

Centrifugal ultrafiltration is a well-established method for concentrating and purifying DNA. Here, we describe the use of centrifugal ultrafiltration for the separation of plasmid DNA isoforms based on differences in elongational flexibility of the supercoiled, open-circular, and linear plasmids. Transmission of each isoform is minimal below a critical value of the filtration velocity, which is directly related to the magnitude of the centrifugal speed and the system geometry. A discontinuous diafiltration process was used to enrich the desired isoform, as determined by agarose gel electrophoresis. The simplicity and efficacy of this membrane-based separation are attractive for multiple applications requiring the use of separated DNA isoforms.