Liquid Biopsy for Investigation of Cancer DNA in Esophageal Adenocarcinoma: Cell-Free Plasma DNA and Exosome-Associated DNA.

Liquid biopsy of cancers is an area of increasing interest in medical practice for the surveillance, management, and potential detection of malignant cells, using minimally invasive collection of body fluids. A liquid biopsy is particularly useful for metastatic cancers, which may be difficult to be sampled by core biopsy, due to difficulty of access or an occult location. Access to DNA shed from esophageal adenocarcinoma can enable the detection of mutations confirming the presence of malignant cells or the evolution of clonal lines with altered treatment response profiles. In this chapter, we detail a method for the isolation of cell-free DNA from blood plasma and DNA associated with exosomes in blood from patients with esophageal adenocarcinoma.

Analysis of nucleotides binding to chromatography supports provided by nuclear magnetic resonance spectroscopy.

The epitope mapping of nucleotides bound to three chromatography supports is accomplished using saturation transfer difference (STD)-NMR spectroscopy. This experiment involves subtracting a spectrum in which the support was selectively saturated from one recorded without support saturation. In the difference spectrum only the signals of the ligands that bind to the support and received saturation transfer remain. The nucleotide protons in closer contact with the support have more intense signals due to a more efficient transfer of saturation. We investigate the effects on the binding to the nucleotides by the introduction of a spacer arm between l-histidine and Sepharose. Our NMR experiments evidence a clear contribution of the spacer to the interaction with all the nucleotides, increasing the mobility of the amino acid and giving different STD responses. This enhanced mobility originates the reinforcement of the interactions with the sugar moiety and phosphate group of 5'-CMP and 5'-TMP or the base of 5'-GMP and 5'-UMP. Hence, with this study we show that by using STD NMR technique on chromatographic systems it is possible to provide a fast, robust and efficient way of screening the atoms involved in the binding to the supports.

A framework for the prediction of scale-up when using compressible chromatographic packings.

Experimental data are given for the solid pressure distributions in chromatography columns of various column aspect ratios packed with four types of agarose-based resin. The loss of column wall support at large scales can result in unexpectedly high pressures caused by the compression of the matrix via drag forces exerted by fluid flow through the bed. The need for an accurate model to predict flow conditions at increasing scale is essential for the scaling-up of chromatographic processes and for avoiding bed compression during operation. Several studies have generated correlations that allow for the prediction of column pressure drops, but they either are mathematically complex, which impairs their practical use, or require a large number of experiments to be performed before they can be used. In this study an empirical correlation was developed based on a previously proposed model, which links the critical velocity of operation of a chromatographic system (microcrit), to the gravity-settled bed height (L0), the column diameter (D), the feed viscosity (micro), and the compressibility of the chromatographic media used (micro 10%). The methodology developed in this study is straightforward to use and significantly reduces the burden of preceding laboratory-scale experimentation. The approach can be used to predict the critical velocity of any chromatographic system and will be useful in the development of chromatographic operations and for column sizing.

Development of saxitoxin-conjugated affinity gels.

Saxitoxin (STX) and its analogues accumulated in bivalves cause food poisoning through the blockade of sodium channels in the nervous system. In the current studies, STX-conjugated agarose gels as affinity chromatography reagents were prepared for investigation of the fate of the toxins in natural environments and in the human body. A carboxyl moiety was introduced through positions C11 and C13 to leave the most characteristic part of the molecule intact. Two types of synthesized derivatives, 11-(2-carboxyethylthio)saxitoxin and 13-O-hemisuccinyldecarbamoylsaxitoxin, were successfully conjugated to Sepharose 4B in high yield. Affinity gels containing 500 nmol of STX or decarbamoylsaxitoxin per milliliter of gel were accomplished by masking the residual amino groups by acetylation. Finally, the STX-conjugated affinity gel was effective for concentrating STX-binding proteins from pufferfish and bullfrog plasma.

Direct quantification of intraparticle protein diffusion in chromatographic media.

Diffusion coefficients of proteins in chromatographic media are important parameters for the rational design of stationary phases and purification schemes. In contrast to free diffusion, intraparticle diffusion is hindered by the porous structure of the media. Direct intraparticle diffusion analysis (IDA) is a novel approach for the determination of intraparticle protein diffusion coefficients. IDA is based on the evaluation of spatially and temporally resolved intraparticle concentration profiles. To prevent adsorption and to study diffusion only, the chromatographic media are investigated in underivatized form. With IDA, intraparticle concentration profiles are measured in a microcolumn by confocal laser scanning microscopy (CLSM). From this dynamic data, the diffusion coefficients are determined by parameter estimation, using a spheric diffusion model. The boundary condition is given by the measured protein concentration in the bulk phase. IDA is applied to determine intraparticle diffusion coefficients of seven different proteins in Sepharose 6 FF. The results show excellent congruence of experimental data and simulation results. Moreover, the determined diffusion coefficients lie well within the range of data published in the literature. Given that the material in question allows optical analysis, IDA is a general approach for studying protein diffusion in porous particles and is easily adapted to different proteins, solution conditions and stationary phases.

Robust enrichment of phosphorylated species in complex mixtures by sequential protein and peptide metal-affinity chromatography and analysis by tandem mass spectrometry.

Reversible protein phosphorylation mediated by kinases, phosphatases, and regulatory molecules is an essential mechanism of signal transduction in living cells. Although phosphorylation is the most intensively studied of the several hundred known posttranslational modifications on proteins, until recently the rate of identification of phosphorylation sites has remained low. The use of tandem mass spectrometry has greatly accelerated the identification of phosphorylation sites, although progress was limited by difficulties in phosphoresidue enrichment techniques. We have improved upon existing immobilized metal-affinity chromatography (IMAC) techniques for capturing phosphopeptides, to selectively purify phosphoproteins from complex mixtures. Combinations of phosphoprotein and phosphopeptide enrichment were more effective than current single phosphopeptide purification approaches. We have also implemented iterative mass spectrometry-based scanning techniques to improve detection of phosphorylated peptides in these enriched samples. Here, we provide detailed instructions for implementing and validating these methods together with analysis by tandem mass spectrometry for the study of phosphorylation at the mammalian synapse. This strategy should be widely applicable to the characterization of protein phosphorylation in diverse tissues, organelles, and in cell culture.

Subtractive chromatography for purification and recovery of nano-bioproducts.

A novel polymer-coated adsorbent (subtractive adsorbent) has been manufactured and evaluated for the recovery of nanoparticle bioproducts. The core principle was to coat inert macroporous polymers (e.g. agarose) upon adsorbent beads of varied ligands. Here BSA nanoparticles, with an average nanoparticle diameter 95 nm, were fabricated and selected as feedstock for the demonstration of the principle. The adsorption of a mixture of fluorescently labelled BSA solution and BSA nanoparticles was investigated in a batch binding experiment upon polymer-coated Streamline DEAE and visualised by laser scanning confocal microscopy. The mechanistic design of such adsorbents and their basic application for the recovery of target nano-bioproducts from complex feedstock is strongly indicated.

Hydrophobic interaction chromatography selectivity changes among three stable proteins: conformation does not play a major role.

Interesting retention and selectivity changes have been noted for a number of proteins in hydrophobic interaction chromatography (HIC). In this study, we investigated the degree to which conformational changes may be responsible for selectivity changes of stable proteins. Hydrogen-deuterium isotope exchange detected by mass spectrometry was used to investigate changes in solvent accessibility during adsorption on HIC media. Lysozyme was determined to exhibit EX2 hydrogen exchange kinetics both in solution and adsorbed to Butyl Sepharose 4 Fast Flow and Phenyl Sepharose 6 Fast Flow high sub surfaces. A small, but significant, increase in solvent accessibility was observed upon adsorption. Similar approaches were used to analyze solvent accessibility of three stable proteins with melting temperatures above 50 degrees C exhibiting significant selectivity changes on Butyl Sepharose and Toyopearl Butyl 650M. While all three proteins (lysozyme, chymotrypsinogen A, and ovalbumin) exhibited enhanced exchange while adsorbed, no differences in solvent accessibility on the different adsorbents were observed. More detailed studies of lysozyme showed no significant changes in labeling prior or during elution. These results demonstrate that HIC surfaces examined here do not dramatically alter the structure of these stable proteins and that differences in conformation are not responsible for the selectivity changes observed. Thus, other factors such as different preferred binding orientations or variations between the media pore structure, size, and/or surface chemistry must be responsible.

Development and validation of an affinity chromatography step using a peptide ligand for cGMP production of factor VIII.

An affinity chromatography step was developed for purification of recombinant B-Domain Deleted Factor VIII (BDDrFVIII) using a peptide ligand selected from a phage display library. The peptide library had variegated residues, contained both within a disulfide bond-constrained ring and flanking the ring. The peptide ligand binds to BDDrFVIII with a dissociation constant of approximately 1 microM both in free solution and when immobilized on a chromatographic resin. The peptide is chemically synthesized and the affinity resin is produced by coupling the peptide to an agarose matrix preactivated with N-hydroxysuccinimide. Coupling conditions were optimized to give consistent and complete ligand incorporation and validated with a robustness study that tested various combinations of processing limits. The peptide affinity chromatographic operation employs conditions very similar to an immunoaffinity chromatography step currently in use for BDDrFVIII manufacture. The process step provides excellent recovery of BDDrFVIII from a complex feed stream and reduces host cell protein and DNA by 3-4 logs. Process validation studies established resin reuse over 26 cycles without changes in product recovery or purity. A robustness study using a factorial design was performed and showed that the step was insensitive to small changes in process conditions that represent normal variation in commercial manufacturing. A scaled-down model of the process step was qualified and used for virus removal studies. A validation package addressing the safety of the leached peptide included leaching rate measurements under process conditions, testing of peptide levels in product pools, demonstration of robust removal downstream by spiking studies, end product testing, and toxicological profiling of the ligand. The peptide ligand affinity step was scaled up for cGMP production of BDDrFVIII for clinical trials.

Use of ceramic monoliths as stationary phase in affinity chromatography.

The use of coated ceramic monoliths as support for affinity chromatography is described. Ceramic monoliths are robust active matrix supports and present a very small pressure drop. Monoliths are coated with a very thin agarose gel layer and activated using a standard activation process for agarose beads. Experiments demonstrate that enzyme adsorption occurs exclusively on the outside surface of the agarose coating since enzyme molecules are too large to fit into the porous matrix. Adsorption and desorption rates are large and production of enzyme per unit monolith volume justifies further exploring this separation process for large throughput operation.

Dynamics of protein uptake within the adsorbent particle during packed bed chromatography.

A new experimental set-up for on-line visualization of the intra-particle uptake kinetics during packed bed chromatography has been designed and tested. Confocal laser scanning microscopy was used to analyze the dynamics of protein adsorption to porous stationary phases. In combination with this, a flow cell was developed that could be packed with chromatography media and operated as a fully functional mini-scale chromatography column. Adsorption profiles of single- and two-component mixtures containing BSA and IgG 2a during packed bed cation-exchange chromatography were investigated. The two proteins appear to exhibit different transport characteristics. For BSA a classical "shrinking core" behavior could be detected. The profiles obtained during IgG 2a adsorption point toward a different transport mode, which deviates from the classical pore-diffusion picture. For the two-component system, a superposition of the single-component profiles combined with a classical displacement of the weaker bound protein species was found. The results indicate that depending on the adsorbed protein the uptake can vary tremendously, even for adsorption to the same chromatographic support. It is clearly shown that the new microcolumn allows in situ quantitative investigations of protein adsorption dynamics within a single particle, which adds a new tool to the available methods for characterizing and optimizing protein adsorption chromatography.

Performance comparison of protein A affinity-chromatography sorbents for purifying recombinant monoclonal antibodies.

We describe the performance characteristics of five Protein A affinity-chromatography sorbents (Sepharose Fast Flow, Poros 50, Poros LP, Prosep and Streamline) for purifying a recombinant humanized monoclonal antibody from clarified Chinese hamster ovary cell culture fluid. We measured the dynamic capacity at varying flow rates, maximum capacity, pressure drop and production rate. For purified antibody, we measured yield and purity (by SDS/PAGE, the amount of DNA, the amount of host-cell proteins and the amount of Protein A). We found that, whereas all sorbents provided significant and essentially equivalent antibody purification, there were differences in capacity and pressure drop, which affected the production rate and had implications for process applications.

Continuous superporous agarose beds for chromatography and electrophoresis.

Continuous agarose beds (monoliths) were prepared by casting agarose emulsions designed to generate superporous agarose. The gel structures obtained were transected by superpores (diameters could be varied in the range 20-200 microns) through which liquids could be pumped. The pore structure and the basic properties of the continuous gel were investigated by microscopy and size exclusion chromatography. The chromatographic behaviour was approximately the same as for beds packed with homogeneous agarose beads with a particle diameter equivalent to the distance between the superpores. In one application, the superporous continuous agarose bed was derivatized with a NAD+ analogue and used in the affinity purification of bovine lactate dehydrogenase from a crude extract. In another application, a new superporous composite gel material was prepared by adding hydroxyapatite particles to the agarose phase. The composite bed was used to separate a protein mixture by hydroxyapatite chromatography. In a third application, the continuous superporous agarose material was used as an electrophoresis gel. Here, a water-immiscible organic liquid was pumped through the superpores to dissipate the joule heat evolved, thus allowing high current densities.

Determination of the distribution of selenium between glutathione peroxidase, selenoprotein P, and albumin in plasma.

A chromatographic method is described to determine the distribution of selenium between selenoprotein P, glutathione peroxidase (GSH-Px), and albumin in plasma, using two small columns of heparin-Sepharose and reactive blue 2-Sepharose linked together in tandem. One milliliter of plasma was diluted to 12 ml with 0.02 M sodium phosphate buffer, pH 7.0 (the equilibration buffer), applied to the heparin-Sepharose column, and eluted at a flow rate of 30 ml per hour. GSH-Px was not retained by either of these columns but selenoprotein P was retained by heparin-Sepharose and albumin by reactive blue. After the two columns were separated, selenoprotein P was eluted with heparin from heparin-Sepharose and albumin eluted from reactive blue with high salt. Analytical work confirmed the presence of selenoprotein P, GSH-Px, and albumin in the respective fractions. When rats were injected with 75Se as either selenite or selenomethionine most of the radioactivity was incorporated into the selenoprotein P fraction, with the next greatest amount into GSH-Px, and the least amount into albumin. Slab gel electrophoresis was used to determine that most of the selenium in each of the three fractions was associated with each of these selenium containing proteins. This method indicated that the majority of the selenium in plasma is associated with selenoprotein P, and the only time this was found not to be true was with high levels of dietary selenomethionine.

[Chromatographic properties of human leukocyte alpha-interferon A on sorbents with sepharose and silochrome matrices]. / Khromatograficheskie svoistva chelovecheskogo leikotsitarnogo alpha-interferona A na sorbentakh s sefaroznymi i silokhromnymi svoistvami.

Chromatography on immobilized monoclonal antibodies NK-2 from a bacterial strain-producer resulted in a pure human leukocyte alpha-interferon A (alpha-INF-A) homogeneous upon polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and reverse phase high performance liquid chromatography. The chromatographic properties of partially purified alpha-INF-A on synthetic and commercial sorbents containing immobilized dyes, aromatic dipeptides, chelating and hydrophobic ligands as well as on porous glass have been investigated. In most cases, [125I]alpha-INF-A was used as an inner standard. The chromatographic behaviour of native and [125I]-labeled alpha-INF-A was practically the same. alpha-INF-A was most effectively chromatographed on porous glass, L-Trp-L-Trp-Sepharose 4B and Cu2+-chelate sorbents. In the latter case, the feasibility of substitution of the Sepharose matrix for the silochrome one has been demonstrated. It has been proposed that alpha-INF-A has a hydrophobic "pocket" with exposed aromatic amino acid residues which are capable of selective binding to aromatic dipeptides.